Having traveled back in time 16 years, the immature Hiro seeks out his late mother to try to get his memories back, while Claire has a run-in with a younger Noah Bennett when he was assigned by the company to look after the infant Claire and how she may have become the catalyst for the secret formula. Back in the present, Nathan returns to Pinehurst where Tracy introduces him to a group of U.S. Marines that Arthur has recruited to be his army of super-solders once Mohinder gets the catalyst for the ability-giving formula correct and which hopes the formula will be able to cure his disease... and begin Mr. Petrelli's quest for world domination. Peter and the Hatian return to New York and are sent by Angela in desperate attempt to break into Pinehurst to kill Arthur Petrelli before he can complete the formula. Meanwhile, Ando, Parkman, and Daphne seek out a bicycle messenger who may have the last '9th Wonders' comic book works to learn more about the future and where Hiro is and what to do to save him. Elsewhere, Sylar goes rogue once again by disposing of Elle, and then decides to go after both the heroes and villains to steal their powers for himself.

Following the plane crash, the surviving heroes must team up with one another to try to survive the manhunt. Claire is quickly captured by Noah who takes charge of a "kill squad" to find the remaining people with abilities while Nathan deals with the overzealous 'hunter' Emile Danko whom becomes obsessed with tracking down all people with special abilities in his own lethal way. Mohinder and a powerless Hiro must rely on Matt Parkman's spiritual guide to help them. Daphne makes contact with Ando to help her find Matt, unaware of the people now targeting them. In New Jersey, Syler takes refuge in the house of an agent and tortures him to try to get information to what's going on and he forms an unlikely alliance with the agent's son Luke Campbell. Also, Peter teams up with Tracy to look for help, while she begins having second thoughts about running.

Peter, Matt, and Mohinder drug and abduct Noah "H.R.G." Bennet and hold him captive in a seedy motel room so Matt can interrogate him to find out more about the people hunting them down, but predictably, it does not go as planned as Benett plans to turn them against each other, while Nathan and the sadistic Danko are looking for him. Noah's background story is revealed about how Nathan approached him to help the government's plan to round up people with special powers, and his awkward alliance with Danko who has his own agenda... as does Nathan.

Following a tip from their anonymous source "Rebel", Matt and Peter hurry to rescue Daphne from the holding facilities in 'Building 26' in Washington, and to find evidence that may expose the government's plans to capture those with powers. Meanwhile, Sylar uncovers the truth about his mother after he experiences past memories of his father at a disused diner located deep in the New Mexico desert which makes him dump Luke and head off to look for his biological father. In California, Claire must find a way to sneak Alex out of her house which is under observation by FBI Agents, and Mrs. Bennet reluctantly agrees to help. Elsewhere, Danko hatches another nefarious and explosive plan of his own to trap and kill Matt. Also, Claire has a run-in with an old villain, Eric Doyle, whom she captured a while back who asks for her help to hide from government assassins after him too.

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.