Hiro and Ando find themselves five years after the destruction of New York. People with extraordinary abilities are labeled as terrorists and Sylar, who has assumed the form of Nathan, is the President.

Hiro and Ando set out to find Matt Parkman with his infant son, but soon learn that the infant's powers hinder their travel plans. Meanwhile, the shape shifting Sylar begins to use his new powers to harass Bennet by impersonating his wife, Sandra, knowing he will find out. An angry Matt Parkman begins investigating the sadistic Danko to see revenge for Daphne's death and learns more about his pursuer when he meets his Slavic girlfriend Alena. Mohinder learns more about his father's work about a mysterious place called Coyote Sands in which Angela and Peter make contact with Nathan and Clare where Angela takes them to the remote location where a secret about Angela's past lies buried.

Sylar begins to feel confused and more uncertain about himself when his new shape-changing powers begins to get out of control. He begins to imagine his late mother giving him advice on what to do, while Danko continues to use him to find and kill people with abilities and wants to zero in on 'Rebel'. When Sylar discovers that Rebel is in fact Micah Sanders, he saves him. Sylar decides to change his ways after figuring out that Danko is plotting a so-called 'Final Solution' to exterminate all people with abilities once and for all. Meanwhile, Parkman plans to return to his home in California with his infant son unaware that there are more kill-squad agents after him, Hiro and Ando rashly decide to make a heroic, and probably futile, attempt to make an assault on Building 26.

Nathan and Peter try to find the shape-shifting Sylar before he can make contact with the President and assume his form as well. Clare goes off to try to stop Sylar on her own, only to end up as a captive. Meanwhile, Hiro and Ando make a rash attempt at stopping time so they can break into Building 26. They hope to free those that still survive and have powers, while Danko, framed by Sylar for the murder of an agent, has a talk with Noah Bennett over their views on fighting this war. Elsewhere, Angela meets with Matt to ask for his help to save Nathan, when she has a dream about him being in danger from Sylar.