Three weeks after the destruction of both Primatech and Pinehearst, 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, leading to Claire, Ando, Hiro, Matt, Peter, as well as Tracy to become fugitives from the people who were their former allies.

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.

Claire and her new friend Gretchen investigate the death of Claire's roommate Annie, while Noah comes to Peter for assistance. Samuel and Edgar recover the compass, Hiro realizes his new destiny, and Matt is tormented with mental images from a dangerous foe.

Peter faces unexpected consequences for his heroic acts and encounters a reluctant new hero. As Claire continues to adjust to college life, she must figure out how to deal with her ability having been revealed. Meanwhile, Samuel moves heaven and earth to recapture the memories of his late brother Joseph. Elsewhere, Matt struggles with his internal demons as Sylar mysteriously resurfaces.

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.