Peter finds out that Adam actually wants to unleash the virus and stops him from doing so. Hiro buries Adam alive by teleporting him into a coffin. Monica is kidnapped by a street gang and Niki saves her, but gets trapped in a burning, exploding building. Elle saves Mohinder, Maya and Molly from Sylar’s clutches. Sylar regains his powers using Claire’s blood. Nathan has a press conference to go public with his power, but is shot before he can do so.

Adam and Peter learn that the Shanti virus is in Texas. Sylar kills Alejandro, Maya learns how to control her power and Maya and Sylar make it to New York.

The Bennet family prepares to go on the run before the Company finds them. Hiro goes back in time and discovers that Adam killed his father. Mohinder sides with the Company and kills Bennet by shooting him through the eye, however Bennet is revived by Claire’s blood.

The episode depicts flashbacks that show what happened between the first and second seasons. Peter is taken prisoner by the Company where he meets Elle until he escapes with Adam and gets his memory erased by the Haitian. D.L. is killed after a new personality of Niki’s manifests. Maya reveals her power, which leads her and Alejandro to America in search for help. In present day, Peter remembers who he is.

Hiro returns to the present. Peter accidentally teleports himself and Caitlin over a year into the future in New York and find that 93% of the world’s population has died of the Shanti Virus. Then Peter accidentally teleports back and meets Kensei, who identifies himself as Adam Monroe. Niki is injected with the virus and Mohinder realizes that his blood no longer works as a cure. Matt defeats Maury and finds that he can control others’ minds.

Peter and Caitlin go to Montreal after they find a plane ticket to there among Peter’s possessions. Kensei betrays Hiro after Hiro kisses Kensei’s love Yaeko.

A woman named Elle Bishop tries to find Peter and kills Ricky with her electric powers. Matt and Nathan visit Maury, who has put Molly into a deep sleep and has been giving her nightmares. Maury escapes and gives Matt and Nathan nightmares. Suresh sends Molly back to the Company for a cure, much to Noah’s dismay.

Micah’s cousin Monica Dawson discovers her own ability: muscle mimicking. Matt enlists Nathan’s help to find the man who has been killing the Company founders, such as Kaito. Matt discovers that his father Maury was among the Company founders. Sylar joins Maya and Alejandro on their journey to New York.

It turns out that D.L. is dead. Niki leaves Micah under the care of his grandmother in New Orleans. Peter gains the trust of Ricky, the leader of the Irish gang, and becomes romantically involved with his sister Caitlin. After eight surgeries, Sylar wakes up in Mexico with Candice. He kills her, but he is powerless. Hiro helps Kensei to become a hero.

Peter uses his powers and agrees to help the people who found him with their thefts. The Haitian reunites with Bennet. Maya kills people without touching them when under stress and then Alejandro revives them. Matt interviews Angela about Kaito’s death. Kensei is revealed to be regenerative.