Sylar goes to the Company and inadvertently releases 12 super-powered criminals in a fight with Elle. Future Peter tries to fix his mistake. Angela takes over the company. Claire learns more about her powers. Hiro and Ando travel to Paris to track down the speedster who robbed them. Maya discovers that Mohinder's injection has changed him. Matt meats Usutu, an African with a familiar power.

HRG and his new partner go to a local bank heist with four villains; including Peter being trapped in one of them. Hiro and Ando track Daphne to Germany, and meet the Haitian. Tracy Strauss goes to New Orleans to find out more information about Niki. Meredith teaches Claire a lesson about fighting. Usutu shows Matt a series of paintings about him.

Peter travels to the future and adopts a dangerous ability in order to try to save the world. Meanwhile, Mohinder struggles with his continuing evolution from the formula, and Hiro and Ando re-unite with an old enemy.

Villains Knox and Daphne are on a quest to recruit Hiro and others to the Pinehearst fold. Angela and the Company are paralyzed from recent events. Peter goes to Pinehearst searching for answers but is stunned to learn who the founder is. Claire and Sandra go on a mission to save Meredith from the clutches of Doyle, a villain with abilities to control people mentally and physically. Nathan and Tracy try to trace their origins with Mohinder's help.

Trapped, Nathan and Tracy must fight to save their lives against Suresh, who has changed dramatically. Elle returns with shocking news for Claire and her family. Meanwhile, Angela tries to convince Sylar to save Peter; Daphne is ordered to kill Matt or she will be killed herself; and Hiro questions Usutu's advice.

Hiro attempts to delve into Arthur Petrelli's past to uncover the mystery behind him creating a rival company Pinehearst and his hatred towards Angela. Sylar stricken by guilt tries to stop his murderous ways with HRG and Elle vying for his blood. Meredith's training goes up in smoke with the arrival of her brother.

Nathan learns of his father's plans, while Flint and Knox launch attacks on Hiro, Ando, Peter, and Claire. Meanwhile, Matt tries to revive Angela, Sylar meets with Elle, and Mohinder begins testing of his newest superpower formula.

Following the showdown against Arthur, Nathan and Peter find themselves pitted against one another, and Nathan makes a decision that will have an effect on the entire world. Meanwhile, Sylar holds Claire, H.R.G., Meredith and Angela hostage at Primatech; Ando, Matt and Daphne try to rescue Hiro and find their only hope may lie in Suresh.

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.

Following a chain of unexpected events, our Heroes are on the run from their latest adversary and one of their own, Nathan Petrelli. After Matt paints a series of prophetic images, the tragic fate of someone close to him is revealed. Elsewhere, Sylar continues his search for his father and encounters a young outcast with information and an ability of his own.