Angela Petrelli enters the Company's basement floor 5, where she sees Hiro Nakamura with his sword through his heart, Matt Parkman with his throat slit, Knox pulling Claire Bennet's head off, and Noah Bennet and Peter Petrelli also killed. She then sees Adam Monroe, a woman resembling Niki Sanders and Tracy Strauss, and Maury Parkman, when Sylar puts his hand on Angela's shoulder from behind. Angela wakes up to realize this was a dream.
Claire Bennet realizes that she no longer feels pain when injured, which she felt was all that remained of her humanity. Claire films herself trying to be hit by a train, but Future Peter, masquerading as Present Peter, intervenes before the impact; he then says that she needs to be careful, but that he also has to be careful with what he says to her, and then teleports away.
Meanwhile, two Company agents, Bianca Karina and Gael Cruz, attempt to capture Sylar. One fires a taser at him. He recovers and kills them both with a small hand gesture.
Tracy enters Nathan's hospital room to offer him a seat on the Senate. Nathan believes that Tracy is Niki Sanders, but she insists that she is not. Tracy leaves, somewhat disturbed, and Linderman appears, confirming that Tracy is not Niki, and advising Nathan to accept Tracy's offer.
At the Company, Elle Bishop finds her father, Bob's body with his brain removed. She then lets Noah out of his cell on Level 5, giving him a gun and telling him that Sylar is in the building. As Noah steps out of the room, Elle is telekinetically thrown down the hall by Sylar, so Noah shoots him several times. However, Sylar regenerates and explains that he's already taken Claire's power. After Sylar flings Noah away, he attempts to take Elle's power by cutting her head open. Elle screams and releases a large electrical discharge that knocks Sylar out and allows the Level 5 prisoners to escape their electronically locked cells.
Future Peter explains to Nathan that he is actually from the future and came to the present to stop him from revealing their powers and prevent the future he came from. Nathan then decides to ask Future Peter if he should accept Tracy's offer, but Future Peter tells him only to make the decision himself. Nathan proceeds to call Tracy and accept her offer as Future Peter leaves.
Tracy, walking to her car in the parking garage, is confronted by a reporter, (cameo by "Hero" William Katt), who tries to blackmail her to get her to admit she is Niki, a stripper from Las Vegas. An angry Tracy grabs him, and her emotions trigger her ability of cryokinesis. She accidentally freezes him solid, and he shatters on the ground, dead. Tracy, horrified, flees the scene as the reporter melts down a storm drain.
Later, Nathan is playing a game of chess with Linderman when a nurse comes in to tell him it is time for lights out, and she comments that he can end a game of chess he's playing by himself. Linderman then reveals that only Nathan can see him.
Hiro and Ando travel to Daphne's apartment in Paris, looking for the formula that she stole. Hiro notices an award of Daphne's for a track meet from when she was young. When Daphne arrives, Hiro offers her the award, which he has now stolen from her, in exchange for the formula. Daphne pretends to agree to the trade, but then attempts to take both items. Hiro stops time, but she holds a knife to Ando's throat, since Ando cannot move, and starts to make a cut. Hiro allows her to get away with both items, but when time resumes, he explains to Ando about the tracking device he had slipped into the award. Ando, however, is notices his neck is bleeding, and is astonished that Hiro let him get hurt.
Maya returns to Mohinder's lab, and witnesses him hanging from the ceiling by his legs. She watches as he jumps down, unharmed, and climbs back up the wall, in an insect type of fashion, and after he explains his new powers, Maya expresses her excitement with the results of his new transformation. They then kiss passionately after Mohinder makes an uncharacteristically rash pass at her.
With Bob's death, Angela becomes the new head of the Company, and her first act is to implement some changes, starting with firing Elle. Noah Bennet, now released, returns to his home and finds Claire, alive. Though relieved to see her, he tells her that he can't stay at home because of the escaped villains and prepares to deal with them, shooting down Claire's offer to partner up. When Claire mentions the possibility of being attacked at home, Noah tells her that he had considered that; to make sure Claire stays safe at home, Noah and Sandra reveal their enlistment of the aid of none other than Meredith Gordon, Claire's biological mother, to protect the family in Noah's absence.
Future Peter teleports to Level 5, where Angela angrily informs him that the villains have escaped. Future Peter wonders how this happened different from his time, and also exclaims that he had trapped the present Peter in the body of one of the escaped villains specifically because this didn't occur in his timeline. Angela berates him about the butterfly Effect and blames him for the deviations he has caused from the future she has seen.
Peter Petrelli, trapped in the body of Jesse Murphy, is forced to accompany the other villains in order not to compromise his true identity. As Flint burns a man alive, and Knox punches a man to death, Peter is forced to watch helplessly.
Mohinder wakes up, next to Maya, and appears to be feeling unwell. He goes to the bathroom and washes his face, and we see a strange affliction to his skin, which appears to be forming amber-colored scales. He questions, "What's happening to me?", as this seems to be an effect of the injection he gave himself to give himself powers.
Angela Petrelli ends the episode by going into the cell Sylar occupies and offers him the comforts that a mother should provide for a child. Sylar denies that Angela is his mother, but Angela persists that she is.