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.

Nathan's plans face exposure as Homeland Security begins an investigation under direct orders from the President of the United States. Sylar and Luke embark on a road trip to find Sylar's father, but are secretly being hunted by Nathan's agents. Life gets complicated for the Bennet family as Claire goes into action to protect a young man with abilities from being captured by HRG. Elsewhere, Matt's prophetic images lead Hiro and Ando to India and a mysterious ally comes to the aid of our Heroes

While being held hostage, HRG is subjected to Matt Parkman's unique brand of interrogation, revealing how he became involved with Nathan's government plot to capture those with abilities. Meanwhile, Matt's discoveries bring Peter face-to-face with "The Hunter"

After receiving a tip from "Rebel", Matt and Peter race to Building 26 to rescue Daphne and recover files that will expose the government's plans for those with abilities. Claire finds help from an unlikely source in smuggling Alex out of the city. As Sylar and Luke continue their road trip, Sylar begins to have memories of his father that lead him to the truth about his mother. Meanwhile, "The Hunter" puts his own agenda into action with an explosive surprise for one of our heroes.

When Sylar comes face-to-face with his long lost father, the reunion proves to be what he least expected. Elsewhere, after receiving a tip from "Rebel", Claire must decide if she will help her sworn enemy, Eric Doyle, evade capture. Meanwhile, as "The Hunter" plans to uncover the Petrelli family's secrets and take control of Nathan's operation, Matt finds himself in the spotlight and on the verge of leveling Capitol Hill.

HRG convinces Emile Danko, a.k.a. "The Hunter", to release Tracy from Building 26, in hopes that she will lead them to "Rebel". As Angela evades capture, she turns to an old friend for help. In Los Angeles, Hiro and Ando continue on their latest mission from "Rebel" to protect the newest hero.

Now that Nathan’s ability has been revealed and he has lost control of his operation, he and Claire go into hiding in Mexico. With Emile Danko now in control of the government operation, his plan to destroy everyone with abilities is set into motion as he teams up with an unlikely partner. Meanwhile, Angela and Peter seek refuge in a church and begin to mend their broken relationship.

As Danko spearheads the government operation, someone close to him is put in the line of fire. HRG’s life continues to spiral out of control and his marriage is dangerously close to the breaking point. Meanwhile, Hiro and Ando continue their road trip with a special delivery for Matt Parkman. Elsewhere, Angela Petrelli unearths the demons of her past.

As Nathan, Claire, Peter and H.R.G. help Angela uncover her past, she reveals the dark secrets that have haunted her for years. Meanwhile, Mohinder learns of his father’s involvement in a long forgotten government operation.

Sylar continues his unusual partnership and begins to have an unexpected identity crisis. Hiro and Ando take measures toward bringing down Building 26. Meanwhile, Matt’s new found fatherhood changes his priorities. Elsewhere, Nathan sets a plan in motion to right the wrongs of his government operation.

Nathan faces off against Sylar to keep him from meeting the President. Sylar has his own plans for his new partner. Meanwhile, Hiro learns that there are repercussions to regaining his ability. Elsewhere, Matt is forced to go to extraordinary lengths to protect his future with his family.