As Christmas draws near, Lois receives a call from an anonymous man claiming that Chloe is attached to a bomb, and the only way he won't let it blow is if she reports the truth of Lex's atrocious experiments about the mysterious 33.1. Lois tries to find a way on her own to stop the mysterious person who is linked to both Lex and Grant Gabriel. Chloe and Jimmy end up getting stuck in an elevator at the Daily Planet with the bomb ticking, prompting Chloe to reveal her secret meteor-rock power of healing to him. Meanwhile, Clark returns from his enforced imprisonment from the Fortress of Solitude. With Kara still missing, Clark uncharacteristically wants Lana to re-open her Isis program of spying on Lex with the intent of taking him down, and wants to become closer to Lana when he has been distancing himself from her. But what exactly does 'Clark' have in mind?
- Lois Lane and Grant Gabriel are kissing in a storage closet in the Daily Planet. She tells him that she doesn't want to write the Lex Luthor exposé since it might raise eyebrows about her relationship with Grant. However, Grant says that Lex requested her. Meanwhile, Chloe Sullivan is trying to call Clark Kent, who has been missing for two weeks. Chloe has been covering for him in his absence, explaining that he is in Minnesota, but she is starting to get worried. Lois catches up with Chloe, who gives her all her research on LuthorCorp. While looking through the papers, Lois hears a phone ringing. Despite the fact that it doesn't belong to her, she answers it and hears a mysterious caller tell her that Chloe has a bomb on her. If she doesn't stop ignoring him, Chloe will die.
At the Luthor Mansion, Lex is fencing with Grant. Grant asks Lex to request that someone else besides Lois write the article since Lois has a way of uncovering significant facts, but Lex denies having anything to hide. Even though Grant seems to be concerned, Lex affirms that he always wins.
The caller, whose name is Adrian Cross, is talking to Lois, telling her that he is an escaped clone from LuthorCorp. His body is aging at a rapid rate and he expects to die very soon. While she is talking to him, Lois attempts to send Chloe an e-mail to warn her, but her internet line is cut. Adrian calls her again and warns her not to disobey him. Frightened, Lois looks around the basement of the Daily Planet for men on phones. She spots a suspicious-looking delivery man and follows him into a secluded room, then attacks him. However, the man is innocent and he begins to walk away. He falls back toward Lois, dead from being stabbed with a pair of scissors. Lois' cell phone rings and Adrian warns her to keep her mouth shut.
Clark suddenly reappears on the Kent Farm to find Lana in the barn. He reveals that he was unable to find Kara. Lana tells him she has decided to stop obsessing over Lex, but Clark says he wants to see what she's uncovered. She takes Clark to her secret room in the Isis Foundation, now filled with non-functioning surveillance equipment. Clark finds a folder on Project Scion and Lana shows him the vial filled with black liquid that she thought she destroyed when she wrecked his lab. Clark tells her that she couldn't have destroyed alien technology, so she decides to show him more.
Lois is still attempting to warn Chloe about the bomb. This time, she tries to get a woman to deliver a manila envelope to Chloe which has the warning written on the back. The woman hands the letter to Chloe, who tells Lois that Clark is back and she is leaving to go visit him. At this time, Lois receives a text message from Adrian, warning Lois not to tell Chloe anything. Chloe suspects that something is bothering Lois, but Lois doesn't say anything.
Lana takes Clark to a LuthorCorp lab where Project Scion was tested and shows him Casey Brock, a woman who was found suffering from toxic levels of metal poisoning. Overnight, the amount of metal in her bloodstream dropped dramatically, meaning that whatever was in her bloodstream had left. Clark states that her incoherent speech patterns are actually Kryptonian and writes down what she is murmuring.
Jimmy and Chloe both get into an elevator and share an awkward moment. They recall a Christmas party last year, when Chloe was still dating Jimmy. Chloe turns the envelope over and reads Lois' warning message about the bomb. At this moment, the elevator suddenly brakes, trapping Chloe and Jimmy with the bomb.
Meanwhile, Lois notices an "out of service" sign on the elevator. She begins to walk toward it, but is stopped by Adrian, who is holding the detonator in his hand and demanding his story. In the elevator, Chloe empties her pocketbook to search for the bomb. She finds It, disguised as Chloe's Secret Santa gift. Back in a Daily Planet office, Lois is showing Adrian her article about LuthorCorp's first clone. Adrian tells her about his family and his Christmas memories, then reveals that they were all fictitious memories downloaded into his brain. Lois promises to publish the story if Adrian will let Chloe go, but Adrian has another mission for Lois. She must force Lex to confess what he's done. Chloe is trying to call Clark in the elevator, but Jimmy is annoyed that Chloe would call Clark before she would call 911. The cell phone breaks when Chloe accidentally drops it.
Lois goes to her interview with Lex wearing a hidden camera and a device in her ear which allows Adrian to talk to her. If she can't get a confession from Lex, Adrian will kill Chloe. At the same time, Clark and Lana go to the Daily Planet to see if Chloe can translate the code that Casey Brock was mumbling, but they can't find her.
Grant and Lex are both waiting for Lois, but they are surprised with her first question, a demand to know about Project Gemini. Adrian is still communicating with her through her earpiece, telling her exactly what to do. Lex claims he doesn't have anything to do with cloning and he denies knowing a man named Adrian. Adrian orders Lois to aim a gun at Grant to get Lex to confess. Lois begins ranting about Adrian's life story. Lex knocks her out and finds the hidden camera she was wearing. Shortly after, Adrian enters and tells Lex and Grant about more of his memories. Grant soon realizes that they have the exact same memories, even talking about their past experiences simultaneously. Adrian also says that they have the same DNA and history, only Adrian was a failed experiment and Grant was a successful one. In an outburst of anger, Lex shoots and kills Adrian, saying he was just a mistake. In his last seconds of life, Adrian presses the button on the bomb's detonator.
In a state of panic, Chloe and Jimmy bang on the elevator door, but no one can hear them. Thinking she is about to die, she confesses to Jimmy that she is a meteor freak. They share one last kiss as the detonater ticks down to the final seconds. In the basement of the Daily Planet, Lana turns on Lois' computer screen and sees the email that Lois attempted to send Chloe, warning her about the bomb. Clark uses his super-hearing to locate the sound of the bomb, then he runs to the staircase, soars to an upper floor and superspeeds to the rescue. He opens the elevator door and finds Chloe and Jimmy kissing before he throws the bomb off the building roof, where it explodes harmlessly. Chloe and Jimmy are stunned to find that they are unharmed with the elevator doors open and many people staring at them.
After Lois wakes up, Lex tells her that Chloe is fine, but Lois says she will expose his project to the world. Lex retorts by telling Lois that she has no evidence, and he recently bought the Daily Planet. Since he is now Lois' boss, there is no way she can write the article.
Jimmy catches up with Chloe and they talk about what happened. He wishes Chloe trusted him more to tell him about her meteor infection, but Chloe just says she had trouble accepting herself. Chloe demonstrates her powers for him by healing a cut on his finger. Even though this was not a major injury, Chloe still feels some slight internal pain from using her healing powers. Jimmy promises to keep Chloe's powers a secret.
While Lex is receiving the acquisition papers for the Daily Planet, Grant enters his office, sarcastically congratulating him for purchasing the Daily Planet. He is sick of always being under Lex's control and is outraged for being nothing more than an experiment. Lex declares that all he wanted was a family, but Grant is anxious to break free from his control.
Later, Grant visits Lois at the Talon apartment. Contrary to her first impression, she is not fired, in fact, Lex requested that she stay. Grant then breaks up with Lois, since he thinks their relationship is too complicated, especially after what happened today.
Back at the Kent Farm, Chloe and Clark discuss the possibility of the Brain InterActive Construct's return. The Kryptonian code Clark wrote down was an error message that a system encounters when it can't boot up. Each time the code repeats, it learns from its mistakes and is getting closer to actually loading. Clark warns Chloe that the black fluid has evolved into technology willing to kill. Once Chloe leaves and Lana returns home, Clark and Lana share a warm moment. As they embrace, Clark's face flashes white and his skin distorts, revealing that "Clark" has actually been Bizarro the entire time. Meanwhile, the real Clark is frozen in the Fortress of Solitude.