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.

Claire, back home in California, begins attending college, but is having difficulty adjusting when a mysterious death of a student during the orientation puts her back in the spotlight. In Japan, Hiro and Ando continue their quest to help people with abilities and go so much as to advertise themselves. Meanwhile, Angela fears Nathan/Syler will discover his true identity. Matt tries to settle down back in Los Angeles and raise his son and not worry about unexpected visitors. Elsewhere, Peter is using his ability for good when a mysterious carnival clan, led by Samuel Sullivan, arrives in town which could spell trouble for him and everyone else.

Samuel continues searching for the whereabouts of the soul of his brother. He begins to focus on Peter by using his ink-transparency powers to investigate Peter. Meanwhile, Claire deals with her secret being outed when Gretchen pressures her to tell the truth. But Noah, comes for a visit and immediately suspects that Gretchen knows about Clair's power. In Los Angeles, Matt Parkman continues dealing with Sylar's ghost taunting him and it hinders his latest case of trying to nail a suspected drug supplier. Also, a new 'hero' with powers is introduced; a young deaf woman named Emma, a dispatcher who works with Peter at the New York hospital, whom discovers that she can 'see and hear' sound breaks.

Claire is determined to get to the bottom of the Sorority Rush attacks on her own, until H.R.G. intervenes only to realize he may be the source of her troubles. Meanwhile, Peter's new ability is a perfect fit for his job and gives him the opportunity to help Emma accept her new life. Elsewhere, Sylar's battle at gaining full control over Matt's body escalates -- with potentially dangerous implications at stake.