Volume II of Heroes begins as Peter, Nathan and Matt's fates are revealed. As everyone tries to move on following the showdown between Sylar and Peter, a new force emerges that's working against the heroes. H.R.G. relocates his family to California and tries to live with Claire under the radar, but that proves to be harder than expected. Meanwhile, Hiro finds himself in feudal Japan where he meets his hero Takezo Kensei. Elsewhere, twins Maya and Alejandro Herrera try to get into the U.S. by crossing the Mexican border in order to get help with their deadly abilities.

With one person dead, Matt goes to an unlikely source for help as attacks continue. Claire finds it difficult to hide her abilities at her high school after a fellow student with a secret nearly jeopardizes her cover. Maya and Alejandro's abilities become a threat to others as they cross into Mexico. Meanwhile, Hiro, still in feudal Japan, tries to fix any damage his presence in the past may cause the future; Suresh has to track down the Haitian; and another lost hero joins an Irish gang in order to find clues to unlock his past.

West and Claire exchange secrets' Maya is forced to use her abilities to get Alejandro out of prison. Hiro in the past makes contact with Ando in the present day. Sylar finds himself recovering on a beach with a new ally. Niki and Micah go to visit a relative, while Peter helps out the Irish gang. And Suresh returns to New York and finds a previously undiscovered Mendez painting that foreshadows the death of someone dear to him.

At a local fast food restaurant, Monica Dawson begins to experience some new abilities. Angela Petrelli makes a shocking confession as new information concerning past heroes is revealed. Matt has Molly locate the boogyman on a map, but the results are terrible for everyone. Across the border, Maya and Alejandro make a startling discovery.

In Ireland, Peter tries to move beyond his past, but soon discovers that Elle, a mysterious woman, would go to any length necessary to find him. Matt strikes an unexpected ally to head with him to Philadelphia to find the boogyman following Molly being attacked. Meanwhile, Suresh has a meeting with his new partner and receives a disturbing assignment; Monica tries to adjust to her life as a hero; H.R.G. has to go to lengths to protect his family; and Hiro continues to try to fix the past while Ando tries to put together what happened to his friend.

Suresh must examine his values while working with the Company while H.R.G. travels to the Ukraine to visit a Russian mentor with information on the missing paintings. West helps Claire teach the head cheerleader, Debbie, a lesson after telling Claire she's not extraordinary enough to be on the squad. Meanwhile, at the U.S. border, Alejandro becomes suspicious of Sylar; Peter and Caitlin head to Montreal to find the doorway in Peter's picture, and their findings leave them with more questions than answers; and Hiro's feelings for Yaeko may have ruined history forever.

Peter and Caitlin are thurst into a terrible situation after another one of Peter's abilities reemerges, and they witness first-hand how deadly the virus attacking those with abilities can be. Matt, Nathan, Niki, Suresh and Bob all work together to battle Molly's nightmare man. Despite Claire's efforts to keep her father's identity hidden, West uncovers the truth. In feudal Japan, Hiro and Kensei's journey takes its final turn.

The series flashes back to the events of the four months between the end of season 1 and the beginning of season 2, as Alejandra and Maya begin their journey to the U.S., Peter and Nathan's final fate is revealed, and the details of D.L.'s death are shown.

Bennet, worried that The Company is about to find them, prepares his family to go on the run, but Claire has other ideas. Hiro returns to the present from feudal Japan and learns his father's fate. While grieving, Hiro transports himself back into the past and makes a shocking discovery. Meanwhile, Matt has difficulty expanding his abilities and confronts Angela Petrelli about who really killed Kaito.

After tracking down the last person in the company photo, Peter heads to Primatech Paper in Texas with his new ally to destroy the virus that will kill 93 percent of the population if not stopped in time. Niki returns to New Orleans and meets with Micah, while Monica pushes her abilities to the limit. Hiro sets out to find his father's killer, while Maya must choose between her brother and Sylar.

At Primatech Paper in Odessa, Texas, Peter and Nathan reunite, but the tender moment turns violent when the Petrelli brothers, Matt and Hiro all butt heads due to Adam and his pursuit of the Shanti Virus. In New Orleans, Micah turns to Niki to help save Monica from a deadly street gang. Meanwhile, Maya sees Sylar's true colors when he kidnaps Molly and Suresh, and Elle must be a hero to win back her father.