Season 3, Episode 17: Chapter Four 'Cold Wars'

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.

Season 3, Episode 16: Chapter Three 'Building 26'

Imprisoned inside the super-secret 'Building 26' which is Nathan's base of operations to experiment and terminate people with abilities, Tracy struggles to survive various "heat" experiments as well as wait for an opportunity to try to escape. While the ruthless Hunter Davko obsessively continues to track down the heroes with the obsession of killing them all, Nathan deals with the President of the USA who begins to investigate Nathan's activities and tactics to hunt down the "targets". Meanwhile, Syler continues his quest to locate his biological father with both help and inference from Luke Campbell, as well as government agents now after both of them. Hiro, Ando, and Matt travel to India to find a new ally with abilities to help them survive. In California, Claire faces the wrath of her father.

Season 3, Episode 15: Chapter Two 'Trust and Blood'

Following the plane crash, the surviving heroes must team up with one another to try to survive the manhunt. Claire is quickly captured by her own father who takes charge of a "kill squad" to find the remaining people with abilities. 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 tries to get information to what's going on. Also, Peter teams up with Tracy to look for help, while she begins having second thoughts about running.

Season 3, Episode 14: Chapter One 'A Clear and Present Danger'

Two months after the destruction of both the Primatech and Pinehurst, and the death of Arthur Petrelli, the now-villainous Nathan returns with a vengeance by persuading the U.S. President and the government to round up all people with abilities for containment and disposal, leading to Claire, Ando, Peter, as well as Tracy to become fugitives from the people who were their former allies. In Japan, a powerless Hiro tries to live through the super-charger Ando as his latest partner. In New York, Peter struggles to find a life for himself as a paramedic, but finds that his cannot hide from his past. Claire learns about Nathan's and Angela's plans for interment of people with abilities and sets out to warn Matt Parkman who learns more about his abilities from the spirit of the African spiritualist Usutu. Elsewhere, Syler travels to Baltimore to locate his long-lost father and ends up being the only one who escapes from a government dragnet led by a mysterious agent known only as 'the Hunter'. Mohinder also learns that he has been targeted, and that Noah Bennett is apparently working with Nathan as well.