Deep in the Amazon jungle, a horde of killer ants is destroying everything in its path. MacGyver helps his entomologist friend and the plantation owner to battle the ants before the plantation is destroyed.
MacGyver is assigned to protect a person in the Federal Witness Protection Program. The man he is protecting wants to come out of hiding to visit his dying mother. MacGyver must protect him from the Mob and from the Feds.
MacGyver is kidnapped by enemy agents to retrieve sensitive information he stole from them. To get him to talk, they inject MacGyver with a hallucinogenic drug that will kill him in six hours, unless an antidote they have is administered.
A cruise ship is the target of a terrorist attack and has three bombs hidden aboard. MacGyver and a friend from the agency are asked to dismantle the bombs before it's too late for the crew and passengers.
In Bulgaria, MacGyver collects a top-secret microfilm and attempts to smuggle it out of the country. At the airport he meets a mysterious beautiful American girl, who turns out to have ties to the Bulgarian Secret Police.
While on a rescue mission in Soviet Afghanistan, MacGyver is shot and wounded. An Afghan woman and her son risk their lives to give refuge to MacGyver. A wounded MacGyver must now outwit the Russian Army to complete his mission.
A Russian defector is helped by MacGyver to seek asylum in the U.S. Meanwhile, after Penny Parker comes to stay at MacGyver's for a few days, she accidentally uncovers an assassination plot of a foreign official.
A pregnant woman is on the run from her husband who wants her dead after she discovers his dark secret. MacGyver becomes trapped with the woman in an abandoned factory with her delivery inching nearer.
While MacGyver is at the viewing of this friend, Jack Dalton, two CIA agents gone bad show up to make sure Jack is dead. MacGyver is surprised to find out that Jack really isn't dead and that he is wanted for murder.
A pilot is on trial for being a spy in a Central American country and MacGyver is sent to rescue him. Matters become complicated when MacGyver discovers the pilot's daughter has stowed away on the rescue mission.
An insurance investigator friend of MacGyver's is killed by a diamond thief with diplomatic immunity. Nikki Carpenter, the friend's sister, is teamed up with Macgyver against his wishes to get the diplomat deported.
MacGyver goes to a small town in Arkansas to bail Jack Dalton out of another predicament. MacGyver ends up getting arrested along with Jack and sent to a prison camp where there are forced to dig in an abandoned mine for hidden millions of dollars.
When a satellite carrying a genetic experiment crashes to earth MacGyver is sent in to recover it. When he arrives he discovers that the experiment mutated in space and now ages animals at a vast rate. It is taken back to the lab but the scientist in charge doesn't want to destroy it.
MacGyver's boss Pete oversees the disarming of a nuclear warhead. A deadly explosion at the disarming facility causes Pete to accept full responsibility and retire from the Phoenix Foundation. However, MacGyver soon suspects that the replacement for Pete is responsible for sabotaging the warhead.
MacGyver agrees to accompany Jack on a flight to bring a rich woman and her recently acquired jewels to France. However, as soon as they land in France they are arrested for theft and regardless of their pleas, accused of complicity.
When MacGyver's research into the wildlife around the planned building site of a marina threatens to cause a shutdown of the project, the owner hires a beautiful woman to persuade MacGyver to change his mind... by any means necessary.
Jack Dalton and MacGyver suddenly become dads when a baby is left in Jack's airplane hangar. They search for the mother of the baby, who used to be a girlfriend of Jack's, and thus there is the possibility that Jack is the baby's father.
In the middle of nowhere, MacGyver gets involved in a car accident. He is luckily found by an Amish family and nursed back to health. MacGyver then helps the Amish community to confront a construction crew that is trying to force them off their land.
A teenage prostitute is trying to leave her pimp and return to her family. As MacGyver helps her to do this, it is revealed that she is also being abused by her father who blames her for the death of his wife.
A downed World War II plane in the Arctic is suspected of containing lots of gold. A joint US-Russian team goes to retrieve the gold but it turns up missing, MacGyver thinks that a US soldier is the man responsible for the crash.
Renegade America service men steal everything that's not nailed down in Thailand, creating a life-threatening situation. MacGyver helps set things right, while helping an old friend get acquainted with a son he never knew he had.
MacGyver trails a friend, Billy Colton, to Africa where he witnesses the cruel slaughter of the endangered Black Rhino. When he joins the activists, hoping to prevent the poaching, Mac meets up with the men behind the scheme - Ladysmith.
A rock-star friend of MacGyver's is filming a video for the Rock Against Drugs campaign. A series of mysterious accidents that occur during filming convinces her that her twin sister is attempting to kill her.
MacGyver is mentoring a troubled high school student who drops out of school to work at a construction site with his dad. While there, the kid discovers that the site may be unsafe when he witnesses a safety inspector being bribed.
MacGyver is serving as a sequestered member of the jury in a racially-charged trial. MacGyver sneaks out to investigate the crime scene, uncovering new evidence, but also landing him in contempt of court.
The infamous Dr. Zito escapes from court during his insanity hearing. MacGyver and the police, including the same officer responsible for Zito's incarceration, are now the victims of Zito's sadistic games.
MacGyver arrives at a wasteland test site owned by Phoenix Foundation. There he finds an envelope waiting for him, containing an audio cassette with instructions to play it. A voice tells that he will be waiting for MacGyver ahead and then proceeds to describe how the area, once busy with living things, died. Even the air is hazardous to breathe. The voice is convinced that this is what will happen to the town of Maple Ridge if constructor Bartlett's City Development Program becomes a reality.
Earl Dent's been paroled and asks MacGyver for help. He gets him a job. But some of his former associates wants him to take them to someone who betrayed them. But Dent refuses so they proceed to frame him and tell him that unless he helps them, he's going down. When Mac hears of this he takes out his old bike and goes and joins them. However Dent's parole officer is following them.
Two guys whack a priest in the head with a metal pipe, drag him into a construction site and proceed to rob him of everything valuable. Meanwhile, MacGyver and a woman are attending a hearing about the homeless situation in the area and start wondering why Father Jim is late. The woman is Rachel, Father Jim's assistant whom he had instructed to say to MacGyver "black and blue" should he be late. It's an old expression from their hockey days, a call for help. Then the word arrives: Father Jim has been taken to hospital in a critical condition. He makes little sense as he mumbles something of Danny and Doc. The police deem it unlikely that the muggers will be caught. Then the doctor comes with the news: Father Jim has expired. It's time for MacGyver to start an investigation of his own.
A man has been killed in broad daylight and Pete is at the scene. A stranger passes Pete by and whispers into his ear: "It's off." When Pete is looking at sketches of the suspects, MacGyver notices that Pete has trouble with his vision. Agent Stams from DXS arrives to meet Pete. Phoenix took on the job of returning Samantha Lora, a political fugitive, to her home country. Samantha's supporters were going to deliver a videotape stolen from San Pablo presidential palace showing summary executions of 200 political prisoners, when they ran into a death squad waiting for them. Pete was supposed to get the tape because they have a 6 p.m. deadline for a media conference about its contents at a local broadcasting station, but the man who has it took off when the death squad appeared and his whereabouts are unknown. Samantha is the only one who knows how to contact him. And for her, Phoenix has arranged a safe place until her transport to San Pablo leaves. Pete and MacGyver go to pick up Samantha when she arrives undercover. Samantha calls the number at which the man with the tape can be contacted. He then calls her back and agrees a time and place where he will deliver the tape. MacGyver gets to be the pick-up man. But underlings of the president of San Pablo are on his tail...
MacGyver steps into a bear trap in the woods while tracking a wolf. Luckily for him, two friendly elderly sisters, who are not friends of bear traps, take him home and care for him. The bear trap will be the least of his problems, though.
MacGyver and the Phoenix Foundation are trying to help a Native American lawyer who's going to court to prevent a power company from building just outside their sacred land. When he loses, MacGyver decides to have some research done via satellite. When the company's rep hears of this, he worries what they might find. In the meantime, the lawyer was about to throw in the towel when an old tribesman talks to him. MacGyver goes to the reservation and discovers that the lawyer has taken arms and is doing what he has to to stop the company. Later, the rep shoots MacGyver in an attempt to frame the lawyer. While the rep chases the lawyer, MacGyver escapes and holes up in an old mine where the old man comes to him. He helps MacGyver and tries to show him what he showed the lawyer. MacGyver, upon seeing it, wonders the vision caused the lawyer to go on a rampage. He tells MacGyver, he probably misinterpreted what he showed him. And he gives MacGyver some information he needs.
A man in security guard uniform, carrying a briefcase, enters a hangar alone. There is a helicopter. The man enters the code that opens a storage room door. Inside the room, he steals a book that says "Stealth Helicopter Operating Manual - Top Secret" and a key-card that opens the helicopter. He replaces the fire extinguisher in the copter with one in his briefcase. Finally, he just flies away in the copter. Elsewhere, MacGyver meets his Jewish godson Jeffrey, who's bar mitzvah is going to be on the following day. Jeffrey's father isn't on the best of terms with his own father, but Jeffrey is convinced that his grandfather will attend the bar mitzvah. Jeffrey entrusts the picking up of his grandfather to MacGyver. Granpa tells MacGyver he has to pick up Jeffrey's present from the post office. He sees a man in a suit, wearing an earpiece, standing in guard outside the post office. He asks MacGyver to pick up the packet that is waiting there, addressed to an alias... There is a tracker inside the envelope, so the suits can see that it is moving. When MacGyver exits the post office, the suit pulls a gun on him... what is going on?
MacGyver arrives at a new neighborhood in a moving truck. A 'hood of surfer dudes, scantily clad roller-blade girls, bikers that look at the scantily clad roller-blade girls instead of where they are driving to, weirdos that come out of their house every morning at the same time, shouting "I am alive! I am free!", a helpful landlord Mel and an aspiring actress Kelly from across the street. Then there are the two rich old men who have nefarious plans for the 'hood. With neighbors like this, there is no need for criminals, terrorists or Murdoc.
There is an arsonist, called Prometheus, loose in MacGyver's neighborhood. Naturally, the Fire Inspector and the police are clueless, and have enlisted MacGyver has to do all the real work to catch the arsonist.
Jesse Colton (last seen in #5.5), is shot while looking for his brother Frank (last seen in #5.3) and MacGyver. Luckily for him, he has a bullet-proof vest. He tracks the man, Egan, who shot him and surprises him and his accomplice. Meanwhile, MacGyver and Frank are tied up in a warehouse next to a bomb with a timer that has just over three minutes left in it. Turns out their last-second escape is just about all MacGyver does here - instead Frank and Jesse do all the action here, with some help from the third Colton, Billy (from #5.8). There's a power struggle in Chinatown and they get involved in it.
Scum exiled from Haiti has settled down in Little Haiti, in MacGyver's neighborhood. They are selling drugs, collecting protection payments and threatening shopkeepers with "Baron Samdi". It's time for MacGyver to enter the world of Voodoo to save the neighborhood. Starting from the kidnapped girl.
While researching his family's genealogy, MacGyver discovers that his family name was disgraced during the Middle Ages. He is then knocked unconscious and, not surprisingly, is transported through dreams to the time of King Arthur (a curious Pete look-alike!). Here he must confront some stubborn knights, convince Arthur that he is a friend, and set out in search of his forefathers.
After outwitting the evil Sir Duncan and escaping the clutches of Morgana, MacGyver and Merlin search for the kidnapped Cecilia. They not only free Cecilia and bring Morgana's wizardry to an end, but they find MacGyver's ancestor as well. Here, the first name of our protagonist is finally revealed...
Pinky, a star of silent films, is showing his films to MacGyver. Pinky hopes that The Phoenix Foundation will preserve his films. Pinky and his friend Karl were also good at building sets and making special effects. There was however, a problem: they were both in love with the same girl and became enemies. Two masked men invade Pinky's house and take his films. Can MacGyver retrieve them?
Rival street gangs in MacGyver's neighborhood are recruiting teenagers to sell crack to get money to buy guns with which to wipe out their rivals. Naturally, MacGyver has to solve the problem. Because there is no problem solving of which is too unrealistic for MacGyver.
Dempsey & Magruta: Law Offices - someone picks their way in there, does some vandalism and goes through the drawers and file cabinets until he finds the file he's looking for. MacGyver pays the bail on a young "graffiti artist". A Rich Businessman in a limo is upset at his underling because he has bought the entire slum area and wants to tear it down but can't because an old lady is contesting the eviction notice served by the underling. The underling calms him down by saying that the Judge threw the case out because the old lady did not have a solid case. It's MacGyver to the rescue again...
MacGyver and his young Chinese friend are again at odds with Chinese criminals over labor regulations. During his investigation, Mac is helped by a photojournalist biker named Sam. It turns out that Sam has more than just a passing interest in MacGyver - he believes that MacGyver is his father!
A prophecy predicts that a resourceful man (MacGyver) from the west follows another man (Jack Dalton) to an Ammukash Valley that is supposed to hold the Fountain of Youth. The Valley is, in MacGyver's own words, "Kabulstan, a very hostile third world country that does not like strangers". The prophecy says that the resourceful man has something to do with the destiny of the people of the valley.