Now on his own, Sylar finally finds his biological father, Samson Gray, a reclusive, lung-cancer ridden taxidermist, to confront him with questions about his past, but soon learns that Samson is not who he appears to be. Meanwhile, Nathan continues to lock horns with Danko over the hunter's tactics to eliminate people with abilities, after he tries to frame Parkman for an attempted suicide bombing. This leads to both Nathan and Danko going behind each others back to unseat the other. Nathan becomes wary about Danko going rogue and the hunter interrogating Tracy, as well as Nathan's mother, Angela, about Nathan's own ability. In California, Claire takes Alex's old job at the comic book store where she is given a message by 'Rebel' to help out her former nemesis, the puppet master Eric Doyle, when he too is targeted by rogue agents. Also, Hiro and Ando return to California where they are led by clue from Rebel... to an infant Matt Parkman.

The identity of "Rebel" is revealed with chilling consequences - Emmy Award-Winner Zeljko Ivanek, Brea Grant and Swoosie Kurtz Guest Star.

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.

Claire attends Nathan's funeral while Peter struggles with his grief in his own way by wanting to seek revenge. Meanwhile, Noah and Lauren interrogate a captured Edgar for information to where to find Samuel's carnival. Elsewhere, Sylar returns to Samuel's carnival where he and Lydia try to find a way to emotionally get inside the killer's head to make him see what is troubling him.

H.R.G. recruits Matt to help him take down Samuel, as they use his long-lost love, Vanessa, to lure him to them, but Samuel has his own plans for Vanessa in the works. Meanwhile, Hiro and Ando go to extreme lengths to save Dr. Suresh. Elsewhere, Peter's introduction of Emma to his mother brings forth visions of a very grim future.

Hiro's life hangs in the balance as his brain tumor worsens, prompting him to subconsciously deal with some of his past decisions. Meanwhile, Sylar pays Claire an unexpected visit to get answers as to why he isn't quite himself. Elsewhere, Samuel's plan to impress his long-lost love, Vanessa, takes a terrifying turn.