Sydney Bristow discovers that her job as an agent for SD-6, a top-secret division of the CIA, is not what she thought it was. Sydney's father, Jack, also tells her the truth about his work and she, enraged, seeks help from real CIA and is hired as their double agent under the command of Agent Vaughn. From now on, her job is really simple: she needs to complete her cases at SD-6 while reporting her findings back to the CIA.
On her first mission as a double agent, Sydney is sent to Moscow to retrieve some stolen files about nuclear bomb. Meanwhile, Will continues to grow obsessed with Danny's death and starts his own investigation even though Sydney asked him not to.
Sydney is sent to Madrid to retrieve a 500-year-old sketch that contains a set of numbers and meets up with her deadly nemesis, K-Directorate agent, Anna Espinosa. Meanwhile, Will digs deeper into the cause of Danny's death and finds some odd information.
Sydney and Dixon are sent on a dangerous case involving the safety of the United Commerce Organization. Francie gets suspicious about Charlie and spies on him. Meanwhile, Will continues to investigate the truth about Danny's murder.
Sydney's cover in SD-6 is put in danger after smuggling a wrong biotech engineer into SD-6 from her mission in Berlin. Meanwhile, Will's investigation into Danny's murder leads him to a woman named Kate Jones, who may have information about the killing. Sydney's starts to doubt where her father's true allegiances lie.
Sydney goes undercover in a mental institution to meet a guy programmed to be an assassin. Meanwhile, back home in LA, Will discovers the true identity of "Kate Jones" and Francie learns the truth about Charlie.
Trapped in the Romanian asylum run by the Russian spy group, K-Directorate, Sydney befriends amnesiac agent Mark Shephard. Sloane and Alliance representative Alain Christophe come to conclusion that SD-6 has mole(s) and plan a trap.
Sydney must undergo an extensive lie detector test to prove her loyalty to SD-6 while at the same time she is trying to find connection between a 500 year old Rambaldi sketch and a machine. In the meantime, Will gets deeper into the secrets while investigating Danny's death.
Sydney's life and cover as a double agent is placed in mortal danger when Sloane starts assuming that she is the mole. Dixon's life is at stake after the mission that went wrong. Meanwhile, Will realizes that his investigation of Kate Jones may be more dangerous than he thinks after he gets a call from the person "on the other side" of her pin.
After she manages to escape a certain death at SD-6 and still manages to maintain her cover as double agent, Sydney is sent on a private island to find new identity of Ineni Hassan, an ex weapon smuggler and previous head of weapons resources of SD-6. Things go south for Sydney after she discovers that Jack got into trouble on a mission in Cuba and in meantime, Will Tippin now focused his investigation on SD-6 whose name he heard for the first time thanks to bug from Eloise Kurtz.
Sydney is sent to Greece to retrieve information about new weapons that are being produced by a young tycoon. Meanwhile, Vaughn plans to report Jack for his apparent involvement in murders of many CIA agents and by doing so, he crushes Sydney's newly found admiration for her father.
When former SD-6 agent McKenas Cole with his crew of bandits take over SD-6, Sydney has to forget her previous plan about quitting the agency and has to focus on her mission with Jack to save their colleagues. In the meantime, as he was about to quit his work on a story, Will Tippin gets an unexpected push to continue from the third party.
Vaughn disobeys the CIA in order to infiltrate SD-6 when he receives a desperate plea for help from Dixon. At SD-6, Cole continues his vendetta against Sloane and his search for device in possession of SD-6. Elsewhere, Will continues his work on story.
After the SD-6 finds out that another terrorist organisation was attacked at the same time as them, Sydney and Dixon are sent to Las Vegas, and later Moscow, to try to find something that will bring SD-6 closer to identity of The Man. All in the same time, Sydney learns some shocking news about Francie's fiancé, Jack tries to be a better father to Sydney and Will begins his journey in discovering SD-6.
Vaughn presents Sydney with a moral dilemma that includes Sloane's ill wife, Emily, in order to fulfill the mission whose outcome is an unpleasant surprise to everyone. SD-6 goes after Will when he comes too close. Meanwhile, Francie is dealing with her broken heart.
Department of Special Research gained interest in Sydney's role involving the page 47 and they began their own investigation regarding it. To save herself, Sydney needs to steal 500 year old Rambaldi codes from Vatican to decipher Rambaldi's prophecy. Meanwhile. Sloane gets suspicious that one of the Alliance's members switched sides and is now working with The Man.
Sydney is heavily questioned by the FBI concerning her past and her current activities at SD-6. Fearing that the FBI might detain her longer, Jack and Vaughn must find a way to make her escape before she blows her cover with SD-6...
After she managed to prove her innocence to FBI, Sydney is sent to Vienna to retrieve data from SD-6 spy in Russian Embassy. There she runs into Noax Hicks, her ex who broke her heart and left her without a word few years earlier. Meanwhile, Sloane promises Sydney to help her find her mother and Jack is losing his mind because of it.
As Sydney and Noah go to Cape Town to get some data on "The Man" , Sloane begins to question where Noah's true allegiances lie when his team finds some suspicious bank activities of his. Vaughn goes to Colombia to get information about Russian assassin known under the codename "Snowman" whose recent mission was to kill Kjasinau, a.k.a. "The Man". While Sydney is getting closer to the truth about her mother, Will and Francie confront her about the airline ticket they found in her coat.
Francie is having a rat problem in her house and gives an inspiring speech about catching them which gives Sydney idea how to catch Khasinau. She and Vaughn set up fake transaction for a Rambaldi artifact with Satk, but their job is compromised when Sloane sends SD-6 agents to steal the presumed second vial. Meanwhile, Will learns the truth about his kidnapping and Jack Bristow has no option but to help him.
While Sloane is desperate to buy few more days for his wife, Will, with a help of Jack, sets up a meeting with his contact "Deepthroat" in Paris. As the luck would have it, Sydney and Dixon will be there at the same time trying to steal a very important document from Khasinau aka "The Man" and his right hand, Mr. Sark, who was just recently in the custody of the SD-6.
Sloane must take a difficult decision in order to get to the Alliance's council. After being captured by Sark, Tippin is tortured by a Taiwanese would-be dentist to extract secrets. Sydney, who has to beware her colleague Dixon, assist her father trying to save Tippin. However, after losing Vaughn when the lab exploded, she is in for a surprise...
Sydney finds herself face-to-face with her long-lost mother, Irina Derevko, whose intentions for her daughter are made chillingly clear. However, Sydney manages to escape and rejoin Jack and Will in their escape from Taiwan. After arriving back in Los Angeles, Sydney continues her search for Vaughn, not knowing if he is dead or alive after being swept away by a wall of water in Taipei. Will's life is forever changed when he learns the truth about SD-6 and Sydney's life as a double agent. Also, Dixon must decide whether or not to inform Sloane of Sydney's suspicious activities. But Jack intervenes and covers for Sydney who later finds Vaughn who helps her try to track down her mother Irina who's searching for a Rimbaldi artifact called 'the Bible.'
After turning herself in to the CIA, Irina won't communicate with anyone - except her daughter. Sydney refuses to cooperate, until a mission goes awry and crucial information falls into the wrong hands. Now, against Jack's wishes, Sydney must face Irina and find out what She knows.
Sydney must travel to Sri Lanka to outwit Sark in order to find a crucial piece of Intel from a computer disk that she recovers from Rabal. Meanwhile, Jack faces Sydney's mother for the first time in almost 20 years in her prison cell to discuss Sydney's well being. Also, Will finally meets Vaughn, and Sloane is haunted by his wife's death when someone begins sending him anonymous letters which have Emily's handwriting on them.
Past demons revisit all the characters as Sloane becomes confused and desperate over clues that his wife may not be dead. At the same time, Will meets a woman who claims to know the truth about SD-6. And Jack tries to convince Sydney that Irina is setting the stage to betray them and will go to any lengths to prove it.
Jack's decision to sabotage Sydney's last mission while pinning it on Irina not only brings him closer to his daughter - it sends his ex-wife to death row. But his foolproof plan begins to unravel when Vaughn begins to put the pieces together - and Sydney makes a startling discovery about her childhood.
Sydney's fury at Jack's present betrayal and past sins leads her father to a desperate act to prove his love for her. Meanwhile, Vaughn - after enlisting Will in a seemingly benign CIA request - learns that a mission He and Sydney engaged in could have disastrous consequences for their health.
As Vaughn's life hangs in the balance, Sydney has no choice but to turn to Sark for help in securing an antidote for the virus. But when Sark demands She help him to kill Arvin Sloane in exchange for his assistance, Sydney faces a decision that could expose her as a double agent.
Sark's alliance with SD-6 suddenly puts Sydney at risk of being exposed as a double agent. She has no choice but to cooperate with his plan, until his alliance with Sloane sends several nuclear weapons into the wrong hands. Now, only Irina holds the key to unraveling Sark's agenda - and She refuses to cooperate.
Still trapped in hostile territory in Pakistan, Sydney, Jack, and Irina continue their search for the missing nuclear warheads held by PRF's leader Gerard Cuvee. After several misadventures, they arrive at Cuvee's stronghold, only to be betrayed by Irina. Back in the USA, Vaughn wants to mount a secret rescue mission to Pakistan before Kendell authorized the Indian army to launch an air strike on the facility with Jack and Sydney held captive inside. Meanwhile, Sloan decides to pay off his unknown blackmailer.
Backed into a corner, Sark cuts a desperate deal Sloane using Sydney to recover a state-of-the-art surveillance system. But when the plan goes awry, SD-6 sends Marshall with Sydney on her next mission... giving the CIA no choice but to extract the op-tech specialist. Now Sydney faces the consequences of "waking up" Marshall - and possibly destroying his life in the process.
When Sydney learns that Marshall has been kidnapped, she struggles against a heartless Sloane to bring Marshall back whom is being tortured by the same Taiwanese torturer Dr. Lee "Suit and Glasses" to uncover the code for the top secret ECHELON security system whom tries to stall for time. Sydney and Dixon are instead sent to Ho Chi Minh City, Vietnam to recover the hard drive for ECHELON. Meanwhile, Kendall and the rest of the CIA frantically tries to prevent SD-6 from gaining access to ECHELON... and Jack realizes that the only one who can help them is Irina.
Sydney and Vaughn reach a crossroads as they try to turn a professional relationship into a personal one during a mission to recover an experimental gyroscope. Meanwhile, Jack struggles to outwit the persistent SD-6 security expert, Ariana Kane, as she tightens the noose of suspicion around him of being Sloan's blackmailer. But Sloan is eventually revealed to know more than he claims: there never was a blackmailer, and Emily is really alive and in league with Sloan to get away from the Alliance!
The entire world of 'ALIAS' is turned upside down. Sloane disappears mysteriously and Anthony Geiger becomes the new head of SD-6. As the Bristows struggle to keep their secrets safe and stay one step ahead of Geiger, Will and Francie make a startling discovery of their own while Francie prepares to open her new restaurant. After an airborne mission, Sydney uncovers a crucial information that could shut down SD-6 and bring down the entire Alliance. But in order to put her plan into action, she must tell Dixon the truth about everything.
When a young CIA agent dies, suspicion immediately falls on her parter and lover, agent Jim Lennox. But after Sydney rescues Lennox from captivity, She trikes up an instant connection as they discover shared wounds - realizing They've both lost someone they love to the job. Yet even her judgment is thrown when Vaughn and Jack discover that Lennox was pursing a technology that allows people to change their appearance. Now Sydney must ask herself: is this the real Jim Lennox - or is his double?
When Sloane gets his hands on a terrifying Rimbaldi weapon that causes internal spontaneous combustion, Sydney must turn to a betrayed and hurt Dixon for help. But when her ex-partner refuses any assistance, She has no choice but to carry out the mission herself. When Sydney is captured, Vaughn must persuade Dixon to help the CIA rescue Sydney from an Afghan warlord's camp.
When Sydney learns that Vaughn is under investigation for being a double agent, Jack and Irina forge an unlikely partnership in their attempt to get their daughter out of the CIA for good. Kendall learns that Sark and Sloane are attempting to get their hands on a Rambaldi manuscript detailing the works of the human heart, so he sends Jack and Irina to Bangkok to learn more, and then to Panama to capture Sloane. But Irina betrays Jack and escapes from custody... this time for real.
Following her betrayal, the CIA try desperately to track down Irina Derevko. Their trail on Derevko leads them to Stuttgart and closer to Sark and Sloane, even as Sloane contemplates giving up his quest to complete Rambaldi's work in order to stay with his wife, Emily.
When the CIA intercepts a secret message, Sydney discovers that the life of Neil Caplan, the mathematician still held captive by Sloane and Irina, may be in danger from the most unlikely source: his wife Elsa whom Jack has arrested, forcing Sydney to try to clear Elsa's name by going on her own mission to Moscow and Spain to try to rescue Neil Caplan. Meanwhile, Sloane becomes obsessed with finding out who accidentally killed Emily, and Sark makes contact with the Francie impostor to locate the person responsible... by using Will to infiltrate the CIA satellite surveillance systems.
As Dixon struggles with the death of his wife, He refuses to take time off from work until Sloane is brought to justice. But Sydney worries that Dixon's repressed rage could cause more harm that anything Sloane could do.
Sydney finds herself racing to clear Will's name when the Francie impostor frames him for the CIA intelligent leak by making him appear to be the other double of the Helix project. But Sark makes matters worse when he sends a team to extract Will, to make it look that he's guilty. Meanwhile across the globe, Irina and Sark discover a stumbling block could turn into an opportunity... with Sydney's cooperation.
Sydney must confront her mother, who tells a clue about "some Rambaldi artefacts" in Zurich, but it was a trap to capture Jack. As Sloane keeps the latter in hostage, Vaughn and Sydney go to Stockholm to capture Sark, who reveals the hideout in Mexico City. Meanwhile, Tippin discovers that Francie is in fact a "double" and is the one who framed him...
Having woken up in Hong Kong, with no memory for the last two years (!), Sydney returns to Los Angeles to try to piece together the last two years of her life and discovers the fates of her friends and family: Vaughn has married thinking that Sydney was long dead; Marshall is having a baby with CIA tech expert Carrie Bowman; and Dixon is now the new division head of the L.A. office branch of the CIA. Sydney also learns the shocking fates of Jack and Sloane; the former is in CIA custody for communicating with Irina whom still is in hiding, while the latter is living in Switzerland under house arrest in exchange for co-operation with the CIA. Sydney is granted temporary CIA clearance on a case that may help her regain her memory and she meets a new enemy group called The Covenant.
Sydney's search for her past leads to an imprisoned Sark, but their Q&A is cut short when he becomes the ransom for a pair of abducted CIA scientists by the Covenant, whose kidnappers may be tied to the murder of his father. Meanwhile, Jack contacts an old friend of sorts for info on Sloane's new world-peace project in Switzerland. Also, Vaughn makes a decision about his future as an operative for the CIA.
Sydney and Vaughn are reunited again as a team to prevent Sark, now a head leader of the Covenant, from destroying the nation's satellite communications system. Meanwhile, Jack must find a way to stop Marshall from uncovering the identity of a murderer suspect whom is Sydney. Also, Sydney accompanies Vaughn and his wife, Lauren, as they meet with Sloane to ask for a favor.
Sydney discovers a link to her missing two years in the form of Simon Walker, the dangerous leader of a group determined on retrieving deadly biological weapons. Meanwhile, Vaughn struggles with his own feelings of jealousy and longing while Sydney is on her mission, aware of the pressures his job is putting on his marriage to Lauren. Jack takes matters into his own hands to protect his daughter, and purposefully revealing Sydney's deadly secret of being a brainwashed assassin for the Covenant during her two-year absence to Dixon in order to preserve her position inside the CIA.
While Vaughn's life hangs in the balance, Lauren butts heads with Sydney after learning the part she played in his stabbing. Meanwhile, Sydney further questions Sloane's allegiances after he is kidnapped by Kazari Bomani, a kingpin in The Covenant. Jack's cover is jeopardized when he meets with Simon to dig up information on Sydney's missing two years. Also, Marshall is sent on his second mission with Sydney, posing as a high-stakes, southern-accented gambler.
Sydney's emotions are turned inside-out when she once again comes face-to-face with Allison Doren, the murdered Francie's doppelgänger, who was presumed dead but is now a key assassin working for the Covenant. Meanwhile Lauren's search for Lazarey's murderer leads her closer to discovering the connection to Sydney, and Sydney begrudgingly is assigned as Sloane's CIA handler.
Jack takes drastic measures to ensure that the NSC never finds out the truth about Sydney's murder of the Russian diplomat Lazarey. But, his actions place a heavy strain on Vaughn's marriage, as Lauren gets closer and closer to the truth about Sydney. Meanwhile, Sydney agrees to go on a mission with Sloane in order to thwart plans to obtain the operating system to a deadly weapon, and she discovers an unlikely ally in the hunt for her missing two years.
When Sydney is taken into custody by the NSC honcho Mr. Lindsey, Jack and Vaughn have no choice but to ally themselves with Sloane to rescue her. But with only hours to spare before she is forced to undergo a radical surgery to recover her memories, they must put together an extraction team, headed by freelance operative Brill. Meanwhile, Lauren faces an impossible choice: side with the NSC who she wants to believe is doing the right thing, or with her husband in their rescue of Sydney.
After making a shocking discovery of a severed human hand in the desert that belonged to Lazarey, the Russian diplomat she murdered while working as a brainwashed assassin for the Covenant, and who may in fact be alive, Sydney agrees to submit to an experimental procedure conducted by an eccentric doctor, named Dr. Brezzel, designed to retrieve her lost memories. But while Jack and Vaughn look on, Sydney's mind proves surprisingly resistant to letting her remember her missing time... and the process of recovering it could end up killing her. Meanwhile, Lauren makes a great sacrifice of allowing herself to get tortured and beaten up in order to make her alibi believable to Lindsey after helping breaking Sydney out of NSC custody. Also Sloane finds himself boxed in by an unlikely enemy, that of Mr. Lindsey, who wants to see Sydney Bristow eliminated permanently.
The identity of the mysterious "St. Aidan" forces Sydney to pull a stunned Will Tippin out of witness protection for help in finding Lazarey to clear her name. But the pursuit sends the two old friends on a collision course with Allison, the Francie impostor who ruined both their lives. Meanwhile, a jealous Lindsey arrests Jack and Vaughn as conspirators in Sydney's escape from NSC custody. Sloane, still under pressure from Lindsey, puts a plan in motion to eliminate Sydney, and Dr. Brezzel has an unpleasant run-in with Sark whom is also looking for Sydney.
In this episode, Sydney finally learns the shocking truth about her missing two years from an unlikely source: FBI Special Officer Kendall. Kendall whisks her away and talks to her from the privacy of an airborne 757 jet. According to Kendall, Sydney was captured by the Covenant after her fight with Francie/Allison, held captive in Russia for over a year and brainwashed to become an assassin. But Sydney only pretended to be brainwashed and contacted Kendall who became her contact and handler, thus giving him information about the Covenant and about their quest for Rambaldi artifacts. Sydney also staged the murder of Andrian Lazarey, and then deliberately had her memory erased to prevent the Covenant from knowing about secrets she had learned about Rambaldi's findings.
Jack contacts a mysterious woman, that of former KGB agent Katya Derevko, Irina's older sister, to help him free Sydney and Vaughn, whose plane has crashed inside North Korea while seeking to find a defecting Russian scientist, named Leonid Lisenker, whom Sark is trying to kill before turning himself to the CIA. But Jack is faced with a curious conundrum when Katya tells him that she will not put the rescue plan in motion until he fulfills a favor: assassinate Sloane.
Sydney and Vaughn are sent to retrieve the Doleac Agenda to gain an advantage over The Covenant. For this, Sydney and Weiss must convince rogue security systems designer Toni Cummings to help the CIA break into a Lethal Response System. Meanwhile, Sark approaches an unlikely ally, that of Lauren Reed, to kill the Covenant's six cell leaders in order to take control of Covenant for themselves at the behest of the a senior leader, the rouge agent McKennis Cole.
While trying to retrieve a bomb, Sydney and Vaughn are ambushed by unidentified assailants. Meanwhile, Lauren and Sark continue to solidify their new partnership as the new leaders of the Covenant. Sloane divulges a dark secret to CIA therapist Dr. Judy Barnett about his past involving Sydney and Irina Derevko. Also, Marshall shows the strains of new fatherhood.
Sydney and Vaughn must convince bomb maker Daniel Ryan that they are part of The Covenant in order to find out where he has hidden one of his devices. But Sydney discovers that her ties to the bomber could lead him on a suicide mission when she learns that Ryan's brother was the murder victim that she killed during her interment with the Covenant, and now Ryan wants revenge.
Sydney attempts to rescue Dixon's kids after they are kidnapped by Sark. Meanwhile, Lauren's status as a double agent for the CIA and the Covenant is put to the test when she learns that she has to work with her father; a wealthy U.S. Senator. When Laura's position is compromised, she and Sark decide to frame Sloane for being the CIA mole.
Sydney and Vaughn must track Kazari Bomani down to get hold of a piece of the Rambaldi puzzle before the Covenant gets their hands on it. Meanwhile, Jack reveals his suspicions to Senator Reed about his daughter Lauren's allegiances, and Vaughn decides what to do about his marriage.
Sydney and Jack warn a disbelieving Vaughn about their suspicions of Lauren being the CIA mole. Meanwhile, Kazari Bomani and Sark take possession of the Rambaldi machine as part of their greater master plan. Sydney and Vaughn must stop a Covenant virus that's crippling medical facilities around the world. Sloane's secret of being Sydney's biological father is revealed to Jack, and Bomani begins to lose faith in Lauren's ability to carry out her Covenant missions.
After finding out that Lauren really is working for the Covenant, Vaughn is told by Jack and Sydney to keep up the facade of a happy marriage in order to keep tabs on his wife's activities. But he's in for a shock when he uncovers the truth about Lauren's mother, Olivia, whom is in league with her daughter over the Covenant's activities. Meanwhile, Jack refuses to help exonerate Sloane of his crimes and put in motion a stay of execution, and a monk discloses the identity of the Rambaldi "Passenger" to Sydney.
After finally discovering the identity of the Rambaldi "Passenger," who is Sloane's illegitimate daughter, Sydney and Jack seek the aid of Sloane, to track the "Passenger" down, first by Sloane meeting with the five key members of a secret government group called "The Trust" to gain access to a Rambaldi device to locate the "Passenger". Sydney then travels to Chechnya to a prison where she finally finds her half-sister, Nadia Santos, an Argentine national and secret agent in hiding. Meanwhile, after learning a secret about his father from Thomas Brill, Vaughn is kidnapped and tortured by Lauren and Sark, who are about to track "The Passenger" down themselves while Dixon, Weiss and Marshall race against the clock to find Vaughn before he is killed.
With the aid of Katya Derevko and CIA imprisoned security systems designer Toni Cummings, Sydney and Vaughn attempt to track down Sloane and Nadia. But Lauren and Sark are also in hot pursuit of them in order to uncover the secrets of Rambaldi. Meanwhile, Vaughn's obsession with tracking down Lauren is beginning to consume him. During a mission to Cuba to uncover more Rimbaldi findings, Sydney and Vaughn turn the tables on an old foe; the Taiwanese scientist and torturer "suit and glasses. Also, Katya expresses her attraction to Jack.
Lauren stages a stunning betrayal by impersonating Sydney and blowing up the CIA offices to steal classified materials, and nearly killing Marshall in the process. But Sark is captured during Lauren's escape, and Sydney decides to play the impersonating game herself to learn where Laura is heading off too. Meanwhile, Vaughn comes face to face with his darkest demons in pursuit of his traitorous wife. Nadia must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact and escape from CIA custody. During a mission to South Africa at a Rimbaldi artifact dig, Sydney has a some help and hindrance from Katya Derevko, as well as a final one-on-one fight with Lauren. Afterwards, Sydney receives a shattering revelation from Lauren that will make her question everything (and everyone) she thought she could trust.
Five months later. Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane whom for limited immunity is co-operating with the APO. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn: about her father having Irina murdered over a year earlier.
Sydney unwillingly teams up with her father to hunt down a modern-day samurai, named Kazu Tamazaki. Meanwhile, Nadia is back home in Argentina and refuses to go back into the spy business. But she is forced to when Sydney's life is jeopardized when she's taken captive by the brutal Tamazaki. Sydney finds out the reason behind Jack's misdeed and Nadia makes an unsettling promise to Sydney to find out who murdered Irina.
Sydney must seduce Martin Bishop, a murderous arms dealer in order to track down a stolen NSA code-breaker. Meanwhile, Vaughn fears for Weiss's life, and Sydney and Jack argue with each other about telling Nadia the truth about her mother's death.
Sydney and Vaughn go undercover to track down a deadly new bio-weapon. Meanwhile, Sydney is concerned about Vaughn not having yet put Lauren behind, and Nadia turns to a Jack to ask for his help in finding out the truth about her mother's murder, who tries to throw Nadia away from the evidence pointing to him.
Sydney and Vaughn go undercover as an arms dealing married couple in a mock-up setting of American suburbia to find a stolen electro-magnetic pulse weapon that when detonated, could bring back the Dark Ages. However, the neighborhood they've infiltrated is not as charming as it seems for the other "happy couples" of this American suburbia setting in Russia could spell trouble for them and their cover.
When Sydney gets bitten on the neck by a missing in action CIA agent, she soon finds out that she has been infected by a experiential hallucinogen, causing her to slowly lose touch with reality. Vaughn and Jack must race against the clock to find an antidote before Sydney puts her life (and others next to her) into danger.
While Sydney and Nadia argue about Nadia's acceptance of Sloane's fatherly concerns, Sloane worries about Nadia's well-being when she and Sydney go undercover as wealthy, irresponsible young Hilton-type heiresses to uncover the whereabouts of a deadly chemical from a playboy arms dealer.
Sloane temporarily steps down as director of his APO task force and gives Jack full authority over the next assignment, which involves Anna Espinosa, the former K-Directorate assassin and Sydney's old foe into racing her to go after stolen classified documents. However, Anna turns the tables on APO when she captures Nadia and forces Sydney to do her bidding. During this time, Sydney tells Nadia about the Rambaldi's prophecy which dictates that "two sisters will fight, and only one will survive." Meanwhile, Vaughn visits the imprisoned Sark and tries to trick him into helping them to catch Anna.
While Nadia is in a coma after being shot by Anna, Sark is taken into APO to help them infiltrate the Cadmus Revolutionary Front and retrieve the stolen bomb, but in return he demands to see Lauren Reed's corpse and that Vaughn open her coffin for him. Sydney learns that the comatose Nadia may be the only person with the Intel they need to intercept the bomb, so Jack is forced to prematurely wake Nadia from her coma, endangering her life, which doesn't please Sloane when he finds out.
Dixon secretly enlists Sydney to help him prove that Sloane is double-crossing the CIA and using APO to steel the Blackwell Index, a master blackmail list, and to reconstruct the Alliance of Twelve. Sydney makes her way into Sloane's house so as to copy the encryption key from his secure phone and crack his phone calls. When Nadia finds Sydney snooping around Sloan's computer, she doesn't tell him, but becomes disappointed in her sister and begins to lose trust with Sydney. Meanwhile, Vaughn discovers something disturbing about his late father when he visits his comatose, dying uncle who makes a remark about seeing his father... recently.
During a mission to Austria, Sydney must protect the life of an American civilian, whom she unintentionally put in danger after she acquires information about a new mini-helicopter to be used as a weapon. Meanwhile, Jack travels to Madagascar to visit with an old friend, the arms dealer Sasha Korjev whom is the mastermind behind the assassin helicopter. Back in Los Angeles, Vaughn uncovers more disturbing secrets about his father of finding a diary with notes written years after his alleged "murder," which straightens his quest to know if his father is really alive.
Nadia puts her own life (as well Sydney's and Weiss's) in danger after failing to unveil her past about her involvement with a dangerous criminal, named Ceasar Martinez from her home in Argentina whom recruited her as an assassin for his gang and wants to relive old times. Meanwhile, Vaughn finds a person who is somehow connected to his father and Nadia as well.
When a mission to Cuba goes wrong, Sydney is attacked and placed in serious danger of being buried alive in a sealed coffin. Back in Los Angeles, Dixon is exposed to a deadly pathogen released inside APO which is currently in lock down due to the toxin and Marshal (not being in the building at the time due to his home life problems), is the only one who can get to Sydney and save her. Only with com link help from Jack, Vaughn and the others at APO, the socially awkward and field inexperienced Marshal has to finish a very important mission on his own before it's too late.
Vaughn and Sydney, searches for Vaughns father, and the word Nightingale. Getting help from her father, telling him that Vaughns father might still be alive. Jack Bristow and Sloane have their own agenda. Following Jack Intel, Sydney and Vaughn goes to Munich. Dressed as a German beer maid, Sydney roughly pursued an investment banker to give her information. They find out that Nightingale is still an active experiment, in an atomic plant in Siberia. They go on a mission to the plant. Which turns out to be very dangerous for both Sydney and her father.
On his own and desperate to find out more about his supposedly-dead father, Vaughn is pressured into a rogue operation for an unknown organization in exchange for information on the whereabouts of his father. He gains more than he bargained for in the deal. Meanwhile, Nadia is meeting with her aunt, Katya Derevko, in order to learn more about her mother, but Sydney doesn't trust Katya's motives.
Sydney and Vaughn tell Jack about Sloane's alleged involvement in Vaughn's search for his father and Irina's contract on Sydney's life. After cornering Sloane, they both conclude that someone is framing him. The APO team set a trap to catch the fake A. Sloane, but they fail. Once they realize what "Arvin Clone" is after, Sloane suggests to step down, temporarily. However, Sydney reluctantly convinces him to stay on the case, since he may the only person able to anticipate "Arvin Clone"'s next move. But Nadia fears that this pursuit may revive her father's past obsession: Rambaldi.
Nadia's former caretaker, Sophia, has been severely beaten. She contacts Nadia and asks to meet her. Sloane is told by Sophia that she was beaten up, because someone is trying to track Nadia down, so he and Jack decide to tell their daughters the truth. It turns out that Elena Derevko, the third and the cruelest of the Derevko sisters, has been surveying both Sydney and Nadia for a decade. Meanwhile, Jack's doctor advises him to tell Sydney about his illness.
Jack's illness has caused him to hallucinate about a cure among other things. As a result, Sydney must recreate the time when Jack was working for the CIA and hid the only man who might be able to help him now. For this, Sydney must role play her own mother. Meanwhile, Sophia moves in with Sydney and Nadia.
Sydney and the rest of the team finally capture the Sloane impostor and bring him to APO where they question him to find a rare Rambaldi orchid whose pollen has some miraculous capabilities with a Rambaldi device. However, the real Sloane must relive a painful memory with his late wife Emily in order to get the Imposter Sloane to reveal the orchid location.
After a tactical group infiltrates the DSR and steals all the Rambaldi artifacts, CIA director Hayden Chase discovers that the alarms at the DSR were disabled from Nadia's computer, allowing the raid to happen. Mrs. Chase shows up at the apartment to question her. Soon Sloane and Jack arrive and suspect that Sophia, who had access to the computer while she was living with Sydney and Nadia, is in fact Elena Derevko. They follow her trail to a dead Rambaldi follower, a stunning betrayal, and a presumed dead family member when in a surprising twist, Sydney and Nadia learn that Irina Derevko is in fact alive.
Rambaldi's catastrophic endgame begins to fall into place as a giant red ball version of the Circumference/Mueller device is found floating over a large city in Russia, driving the citizens mad with violence. After a wounded Dixon reveals that Irina is alive, Sydney, Nadia, and Jack set off to find her. It turns out that Irina had been captured, and then duplicated using Project Helix, in order to give the impression that she was dead. Sydney and Nadia discover Irina being held inside a camp in Tikal, safely in the clutches of Elena's private army. Irina had apparently been working to counter Elena's organization, the Covenant, and actually PREVENT the Rambaldi endgame. Irina is taken to APO and tells them of a page she destroyed, a page that was key to Rambaldi's endgame. Under torture, she finally broke and recreated it for Elena. After a short respite, Sydney, Vaughn, Jack, Nadia, and Irina board a plane parachute down, towards Elena, Sloane, the Circumference....and destiny.
Jack, Sydney, Irina, Vaughn and Nadia parachute into Sovogda, Russa to dismantle the giant floating red ball of the Circumfrence which is turning people into mindless, red-eyed zombies out to kill. Back at APO, Marshall and Weiss try use the Blackwell Index to blackmail the Russian defense minister into giving them the access codes to a Russian satellite before the local authorities plan to drop a nuclear bomb on the city to destroy it and prevent the spread of the contagion, and they also discover that Elena is up linking the satellite. In the ruins of the city, a CIA agent, Brodien (the one whom Sydney rescued from Shanghai in the season opener) reminds them that the Rambaldi device is broadcasting a sub audible frequency that physiologically alters people who drink the water-like fluid that has infected the city's water supply and it is irreversible. At the same time, Elena learns of the APO team's arrival and sends Sloane and her men to go out to kill them, leading to a three-way war between Elena's henchman, the APO group, and the zombies leading to Nadia becoming infecting and having a final one-on-one confrontation with Sydney atop a building with the red ball Circumference in the balance.
After learning that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent for another secret terrorist group called Prophet Five, Sydney begins to question whether their business and personal relationship over the years had all been a lie. When she discovers that she's pregnant with Vaughn's baby, she becomes determined to uncover the truth about him. Meanwhile, because of Jack's past betrayal by Irina, he begins to worry that his daughter may suffer the same fate that he did.
Four months after Vaughn's murder by the traitorous Gordon Dean and his associate Ivan Curtis, a grief-stricken Sydney teams up with Renée Rienne, a French freelance assassin and fugitive on the CIA's most wanted list who knew Vaughn from their past association with Prophet Five, to ask for leads in order to track down the killers before they can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace, as Vaughn's replacement at APO, and Weiss struggles to decide whether or not to accept a promotion that would force him to move to Washington D.C. and leave his colleagues at APO. During this time, Sydney, Dixon and Weiss travel to Amsterdam to track down Curtis who is in the process of buying a potential weapon.
Following the theft of a deadly virus, code named Substance 33, in Turkey, Sydney is forced to partner on a mission with new APO agent Thomas Grace where they and Marshall travel to Prauge to look for the stolen virus container where their paths cross with Rachel Gibson, a spy suspected of being involved in activities against the U.S., has something shockingly in common with Sydney that she's working for a black ops group called The Shed, that is run by Gordon Dean and his murderous associate Kelly Peyton. Sydney and Tom must persuade Rachel to infiltrate The Shed to download Dean's computer files to learn where Substance 33 is being hidden. Meanwhile, Dixon must accompany Sloane, who's given a 48-hour pass from prison to acquire a possible cure for his still-comatose daughter, Nadia, from a scientist in Russia.
While Sloane awaits the outcome of his sentencing for treason, a mysterious associate of Gordon Dean approaches him for a favor in exchange for persuading the judges to rule in favor of acquittal. Meanwhile, Sydney and Tom must try to convince Rachel to help them catch the fugitive Gordon Dean who moves his operations to more secure locations. Sydney and Rachel return to the ruins of the Shed's offices in Prague for Rachel to reconstruction Dean's computer server so Tom and Dixon in the Cayman Islands can empty out Dean's bank accounts. Although they are successful, Dean discovers that Rachel is still alive which puts both her and Sydney in grave danger when they are trapped in a car that's hanging by an electromagnet controlled by Dean and his lethal associate Peyton who threaten to drop the hovering car unless Rachel's location is revealed.
Sydney and Tom travel to Marseilles, France when they discover that Renée has stolen the cryo container which contains the cryogenically frozen body of her supposedly dead father. But they soon find themselves under siege in Renée's warehouse hideout by a group of mercenaries who want to reclaim Renée's father when he awakes up from his cryo-induced sleep... so it appears. Meanwhile, Rachel and Dixon travel to San Francisco to assist Marshall in the break-in of a vault facility to copy files to learn more about Renee's father. Elsewhere, Sloane takes matters into his own hands to get himself back into APO and continue his quest to find a cure for Nadia by influencing/blackmailing a influential senator to let him have full access to the CIA's accessories.
After Sydney and the APO team infiltrates a formal party at the Chinese embassy in India to locate a fugitive arms dealer, named Janos Vak, Rachel is chosen to begin very first solo mission by infiltrating an off-shore oil platform, with com-links from Sydney whose pregnancy now limits her role in missions, to steal some computer software from Janos to gain the location of a new weapon. Meanwhile, Sloan, now back at APO, is in frequent contact with the elusive Gordon Dean who wants him to keep close tabs on APO, leading to Dean sending his lethal right-hand assassin, Kelly Peyton, to recover the computer software before APO does leading to a hand-to-hand fight between Peyton and the field-inexperienced Rachel.
Sloane decides to betray Dean when he learns that Nadia's condition will probably not improve. They meet at a race track in Dubai to exchange a network access card which Sydney and Renee stole in Rome, leading to Dean finally being captured. The APO interrogates Dean for information on Prophet Five. Yet another mysterious stranger asks Sloane to eliminate Dean. Meanwhile, Nadia comes out of her coma for a short time after a nameless nurse leaves her room. Under orders from his new Prophet Five contacts, Sloane kills Dean during a routine reboot of the APO's surveillance network, and APO misses its chance to hack the network, but learns Prophet Five is linked to intelligence agencies around the world. At the end, control of Dean's terrorist cell is given to Kelly Peyton.
An incident concerning a microwave bomb brings APO to send Rachel in Sao Paolo in order to take information about this weapon. However, another person who is named "Bob" is also after this information. Rachel has a fling with him, but back at APO, she finds out that he is Julian Sark. Meanwhile, Jack and an old friend are caught by Lazaré while on a stalking mission. Knowing Rachel has a clue to meet Stark, Sydney must deal with this foe in order to free her father from the hands of Lazaré in Tunisia...
When Kelly Peyton steals some software from a CIA warehouse concerning the late Michael Vaughn, Sydney is soon abducted by Prophet Five agents where she is subjected to a hypnotic state making her flash back to her happier times with Vaughn in order to learn where a supposedly powerful device, called The Horizon, is located. Meanwhile, Jack must team up with Renée to locate Sydney when they captured and torture Aldo Desantis, while the mastermind behind Prophet Five is finally revealed... and why the person has a strong interest in Sydney's unborn daughter.
After escaping from Peyton and her henchmen, and learning she's on a freighter at sea, Sydney goes to the communications room and sends a message to APO routed through the CIA to her whereabouts. Unbeknownst to her, the message is intercepted by a mole at the CIA working for Prophet Five, although APO was able to obtain a piece of the transmission. Wanting to retrieve Sydney, the APO team, Rachel, Tom, Dixon, and Marshall attempt to break into a secured server room located at Langley with the goal of obtaining the remaining part of the transmission. Problems arise, however, when APO is forced to take the hard drive, which triggers an alarm. They manage to escape the situation thanks to former APO agent Eric Weiss who aids them in sneaking past the guards. Although the transmission on the hard drive is corrupted, APO is able to learn who corrupted it. Jack sets a meeting up with the division heads of the CIA and is quickly able to identify the mole. Meanwhile, Tom is revealed to have another agenda when he obtains information about a certain Allan Korman, who was a former German assassin now in a witness relocation program, and who murdered Tom's wife many years earlier.
Now nine months pregnant and on maternity leave, Sydney is surprised when her mother, Irina Derevko, shows up at her front door pretending to be a victim pursued by Prophet Five to get information on the whereabouts of 'The Horizon'. Jack, Sydney and Irina travel to Vancouver to an high-rise office building to steal the Horizon, only to get trapped on the upper floors when Peyton and hit team show up, forcing Jack to do battle with them alone as Sydney finally begins to go into labor with Irina as her labor coach. Elsewhere, while Dixon meets with Renee in Paris for information about The Horizon, back at APO, Rachel, Marshall and Tom agree to cover for Sloan when CIA Director Arthur Devilin arrives to monitor the APO records in the wake of the discovery of Prophet Five mole within the CIA.
One month later, with Sydney on maternity leave, she gets forced back into the field when her old enemy, Anna Espinosa, returns after she's secretly sprung from prison by Peyton who gives her a job offer to work for Prophet Five whose leaders have secretly contact with Sloan to get him to set up Sydney in exchange for getting the cure for Nadia. Anna decides that to get at Sydney is that she needs to go through her friends, leading to Anna to abduct Will Tippen. Sydney, along with APO, is forced to try to find Anna and save Will before he's killed unaware that Prophet Five has bigger plans for Syd, to take a sample of her DNA.
While Sydney and the rest of APO try to learn more about Prophet Five and what their plans for Sydney are, Sloane finally acquires a bottle of serum from Prophet Five as a cure for the comatose Nadia. But Sloane becomes distraught when he learns that for it to work, he must stop Nadia's heart for a full 30 seconds. When the proceeder is successful, Jack becomes suspicious about Sloane's possible involvement with Prophet Five, leading him and Nadia to investigate, while the rest of the APO team continues searching for Anna Espinosa, unaware that she has been duplicated by Project Helix to look like Sydney. Meanwhile, Tom travels to France to meet with Renee to look for a fugitive art dealer, named Moritz, whom has the stolen Rimbalid Page 47 artifact, and learn that it's a fake for the real one has with Sloan all this time. Also, Sydney offers Renee a job at APO, only to have fatal confrontation with Anna/Sydney, while Nadia has her own confrontation with her father over his renewed obsession with Rimbaldi.
Visions trouble Sloane while he works for Prophet Five in deciphering the Rimbaldi Page 47 artifact. Meanwhile, a computer chip is found in the dead Renée's body leading Sydney to try to make contact with Vaughn.
Sloane takes Rachel and Marshall hostage to force them to help him find the Rambaldi clue that he is missing. Sydney, Vaughn and APO try to save them by having Marshall's wife, Carrie, to help out, while Sloan plots with Sark and Peyton to take over Prophet Five for themselves.