In order to change the course of history, a scared and cynical Peter Petrelli travels back in time from four years to the day his brother Nathan revealed the existence of the super-humans and was the one who shot him. In attempting to capture future Peter, Matt Parkman gets teleported to a desolate African landscape. In Japan, Hiro takes control of his father's company when, courtesy of a DVD, he and Ando receive instructions from Hiro's late father about a deadly secret contained in the office safe. Hiro can't help but open the safe and the contents are promptly stolen by a "speedster"; a woman with super-fast speed called Daphne. Meanwhile, Nathan undergoes a religious experience while recovering from the shooting and is offered a new job in Congress by a shady blond government woman named Tracy Strauss, someone who looks remarkably like the late Niki Sanders. Elsewhere, Sylar confronts Claire, whose alone in her house, in a bid to get hold of her powers.

A egotistical and super-charged Sylar goes to the Company to kill all the leaders, and inadvertently releases 12 super-powered criminals from the place's notorious Level 5 prison block during a fight with Elle. Peter, trapped in the body of one of the criminals, is set free as well and is forced to team up with a group for a crime spree. Meanwhile, Future Peter tries to fix his mistake with Nathan, as Angela takes over the company in the wake of Bob Bishop's murder and frees Noah Bennett to help the Company track down the 12 escapees and bring them back or eliminate them. In California, Claire learns more about her powers as she recovers from Sylar's attack. Hiro and Ando travel to Paris to track down speedster Daphne Milbrook who robbed them and learn that she is working for a darker power. In New York, Maya discovers that Mohinder's injection has changed him by making him super-strong, but also altered his personality. In Africa, Matt meats Usutu, an African shaman with a familiar power of painting the future. Elsewhere, Tracy learns that she has the power to super-freeze anyone and anything while dealing with a hounded tabloid reporter seeking any dirt on her and the shady Governor Maldon who are continuing to groom Peter for a position in the U.S. Congress.

As Hiro's life continues to hang in the balance, he distracts himself with saving the lives of others. Meanwhile, Angela tries to help the new "Nathan" remember his past, at the risk of his remembering too much. Elsewhere, Tracy is determined to get her old job back, but soon realizes that she needs to make more of an impact.