Four months after the events of the showdown between Sylar and Peter, new Heroes emerge. These include brother and sister Alejandro and Maya. Hiro remains in the past, but what will come of this? Someone dies and someone isn't dead. Claire and her father and the rest of their family get a new life.

Peter falls in with Irish gangsters who know about his past. Hiro works to contain the damage caused by his journey into the past. Kensei's power will be revealed. Suresh locates and cures the Haitian. Matt investigates the murder of Mr. Nakamura. West comes to know of Claire's powers. Maya and Alejandro enter Mexico and find their powers more of a hindrance than a help.

Suresh finds an undiscovered Isaac Mendez painting that shows someone's death; Maya frees Alejandro from a Mexican jail; in the past Hiro discovers something new about Kensei; and Niki and Micah leave Las Vegas to get away from their past. Claire and West take a little trip.

A woman named Elle is searching for Peter. Ando looks for Hiro in the past. Matt looks for the man in Molly's dreams. HRG takes another step in hopes of protecting his family and himself.

Peter goes on a search. West convinces Claire to stand up to someone. Hiro struggles with his feelings for Yaeko. Suresh has more problems with the Company. HRG tries to locate more of Isaac's paintings. Alejandro doesn't trust Sylar.

Peter and Caitlin learn about the endstage effects of the Heroes virus. Many of the Heroes work together to fight the Nightmare Man. West is shocked to the identity of Claire's father. Hiro and Kensei's journey comes to an end.

The events of the "missing four months" are explored. Maya and Alejandro must go on the run, it is explained how Peter ended up in Ireland and what happened to Nathan, Nikki, and D.L.

Mr. Bennet prepares to move his family when he thinks the Company has found them, but Claire doesn't like the idea. Hiro returns to the present and upon discovering his father's death, travels back in time to stop it. Meanwhile, Matt works to master his new mental abilities.

Peter travels to Primatech in Texas to destroy the virus, but not everything is what it seems. Hiro continues the pursuit of his father's killer, while Matt pursues the last Company member in the photo. Nikki is reunited with Micah but has bad news, while Maya has to choose to remain with Alejandro, or go with Sylar.

In Texas, Peter faces off against former friends due to Adam’s misleading story about the Shanti virus. Micah enlists the help of his mother to rescue Monica. Maya is shocked when she learns the truth about her new friend Sylar. Elle tries to make her father proud.

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.