Niki and Jessica come to peace as they rescue Micah. Hiro teleports Ando back to Japan to keep him safe. The Heroes face off against Sylar. Matt gets four bullets to his chest, Hiro stabs Sylar before teleporting to 1671 Japan and Nathan flies Peter high above New York to detonate.

Hiro’s father teaches Hiro how to use a sword. Candice gets Micah to rig the election for Nathan to win. D.L. kills Linderman, but is shot in the process. Sylar kills Ted. Hiro prepares to face Sylar. Matt and Bennet find the Company’s Walker Tracking System: Molly Walker.

Mohinder is introduced to Molly, who can normally locate any individual, but she has the Shanti Virus that killed Mohinder’s sister many years before. Mohinder uses his own blood to cure Molly. D.L. and Jessica go to Linderman’s office. Ted, Matt and Bennet arrive in New York and reunite with Claire and Peter. The latter gains Ted’s radioactive power.

Hiro and Ando find themselves five years after the destruction of New York. People with extraordinary abilities are labeled as terrorists and Sylar has assumed the form of Nathan and is the President. Hiro and Ando eventually return to the present with the help of future Peter and Hiro finds out that he must kill Sylar to prevent the potential future that they had just visited from happening.

Linderman reveals that his plan for Nathan includes Peter exploding. Linderman also shows Nathan one of Isaac’s paintings, in which Nathan is the President of the United States. Peter and Suresh escape from Sylar, but Peter is killed. Mohinder takes him to the Petrelli’s house where Claire now is and who ends up reviving Peter. Suresh joins the Company. Sylar kills Isaac and paints a picture of himself in which he is the President. Candice morphs into Niki and takes Micah to Linderman. Ted, Matt and Bennet escape from the Company’s captivity and decide to disable the Company’s Walker Tracking System in New York.

Claire and the Haitian go to the house of Nathan and Peter’s mother, Angela who is also Claire’s grandmother. Jessica/Niki returns to her home with D.L. and Micah. Hiro steals the sword that he has been seeking. Isaac paints pictures of himself with his head cut open after being killed by Sylar. Sylar attacks Mohinder and Peter. Bennet is deceived by Candice Wilmer, who works for the Company and has the ability to change her appearance. Nathan confronts Linderman, who promises Nathan that he will win the upcoming election for congress and will be living in the White House in a few years.

Matt and Ted take the Bennet family hostage. Ted loses control of his powers and burns the Bennets’ house. In flashbacks, Bennet is given Claire on the condition that he return her to the Company that he works for (that includes Hiro’s father Kaito) if her powers manifest. Bennet explains this as the reason why he is so protective of Claire. Bennet orders the Haitian to escape with Claire.

Bennet and the Haitian pursue Peter and leave a gun with Isaac. Claude leaves Peter because he does not want to become involved with Bennet again. Ted and Parkman agree to go get answers from Bennet. Peter confronts Isaac about his betrayal and Simone is accidentally shot and killed.

Meredith informs Claire’s biological father—Nathan—that Claire is alive. Meredith blackmails him for $100,000 by agreeing to keep quiet about this, as it could ruin his political career. Linderman gets Niki/Jessica out of prison and employs her as an assassin. Her first job is to kill a man (who has employed Parkman as his bodyguard after he is dismissed from the police force) who stole money from Linderman. Jessica is successful and is told her next target: Nathan. Mohinder unknowingly allows Sylar, who is now impersonating Zane Taylor, to join him on his quest to find those with superpowers.

Sylar escapes from Bennet’s captivity. Claude is convinced that Peter’s loved ones are distracting him. To prove this, they follow Simone who kisses Isaac. Claire meets Meredith in person. Isaac contacts Bennet, whom he had previously met, to tell him about a painting that he had finished that shows Peter becoming invisible.