The Second Coming

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The episode begins four years into the future. Peter Petrelli, who has a scar on his face, is being chased and enters a hangar. Claire Bennet tries to shoot him, but Peter stops time and time travels to the present day. At Nathan Petrelli's press conference, future Peter shoots Nathan, as in "Powerless". Present-day Peter and Matt Parkman chase future Peter through the building, but future Peter appears to have escaped. Peter rushes Nathan to the hospital, and although he dies, he comes back to life after Peter kisses him on the forehead. Peter encounters Matt, who catches him trying to find the gun future Peter hid. Peter's scar reappears, and he tells Parkman that he is from the future and teleports Matt away because he knows too much. Matt wakes up in the desert, with no one in sight. As he walks across the desert, he stops in front of a rock where the picture of the earth exploding is painted. Nathan walks out of the hospital to a church next door. A crew of news reporters follow him, and Nathan gives a short speech about how he was saved by God. Peter leaves, and Nathan gets another visitor: Linderman. The governor of New York learns about Nathan on the television, and tells Tracy, who looks identical to Niki Sanders, that he thinks he has found who he is looking for. Angela Petrelli visits Nathan in the hospital. She knows that future Peter is impersonating his past self, and tells Peter that he got the ability to dream the future from her. Future Peter tells Angela that he put his present day self somewhere safe. At the Company headquarters, in one of the Level 5 prison cells, a bald man screams that he is Peter Petrelli. Noah Bennet is also locked up in an adjacent cell.

Claire watches the news reports about Nathan when Sylar arrives at her home. Claire hits him on the head with a blunt object and tries to escape, but Sylar blocks her with telekinesis, effectively trapping her in the house. While Claire hides in a closet, Sylar finds Noah's files for villians. He decides he will target them as his next victims. He is stabbed by Claire, but he pins her against the wall with telekinesis, and starts cutting open her forehead. This act is his standard procedure, and usually kills the victim; due to Claire's power, she does not die. She remains conscious as Sylar lays her on a table and examines her now-exposed brain, claiming he is looking for answers. Although Claire does not feel the pain, it is obviously a psychologically scarring experience. She asks him if he is going to eat her brain; he tells her: "Claire. That's disgusting." When he finds what he is looking for, he places her skull back on and she heals, surprised he is not going to kill her. He tells her she can never die; and now, neither can he.

In his office at Yamagoto Industries in Japan, Hiro Nakamura tells Ando that he is bored without a quest. A video message from Kaito Nakamura is delivered to his office, which tells Hiro to never open Kaito's safe, which holds a secret. Hiro immediately opens the safe, and finds another video, with Kaito repeating that he was not supposed to open the safe. Hiro finds one half of a molecular formula, which gets stolen by a blur before he can comprehend what it means. Hiro stops time to see that the blur is a trail left by Daphne, a speedster. Daphne moves at normal speed while time is stopped, and comments that Hiro did not stop time completely. She hits him in the face and leaves with the formula as time resumes. Hiro jumps to the future to see how the world is destroyed. He sees Japan in a panic, and himself talking to Ando, arguing about the formula. Future Hiro yells at Ando saying that Ando betrayed him. Future Hiro is ready to strike with his sword, when Ando shoots what appears to be red electricity at Hiro, apparently killing him. Ando takes the formula from Hiro's body and walks away. The sky opens up and the world starts exploding, and Hiro jumps back to the present.

Maya and Mohinder Suresh are at his apartment and he realizes that powers are controlled by the adrenal glands. Mohinder thinks he has isolated something that controls powers, and could give powers to anybody. Maya says the powers are a curse, and asks him to destroy the formula. On the docks, Mohinder considers throwing away the syringe with the formula. Instead, he injects himself, and collapses. Two muggers attempt to accost Mohinder as he lays semiconscious on the ground. However, he exhibits superhuman strength, repelling the thugs. In the background, there is a giant painting of the Earth exploding from the inside - the same picture seen by Matt on the desert rock. In the closing scenes of the episode, Mohinder narrates the William Butler Yeats poem "The Second Coming", the title's namesake.