The second season explores the heroes' lives four months after the events of the first season's finale.
The Petrelli brothers are still alive: Nathan has since lost his career and is now an alcoholic, while Peter has amnesia and is found chained to a shipping crate in Ireland. Peter falls in love with a gangster's sister named Caitlin, and has no desire to find out about his past, until Elle, a mysterious blonde with the ability to manipulate electricity, shows up looking for him. Peter, in trying to discover why he is being hunted, inadvertently travels to the future, making a horrifying discovery: in one year, 93% of Earth's population will be dead.
Hiro is in feudal Japan (his story has not skipped ahead four months), where he assists his lifelong hero, Kensei—who is revealed to be an Englishman with the power of spontaneous regeneration—become the man history meant him to be. However, he finds himself conflicted when he falls in love with the swordsmith's daughter, Yaeko, who is supposed to be Kensei's love interest. In a twist of fate, Kensei betrays Hiro, who decides to accomplish Kensei's tasks for him and fulfill history.
The Bennets have moved to California, where Claire struggles with being normal when she knows otherwise. Noah Bennet is working with Mohinder to infiltrate "The Company", looking for a series of eight paintings depicting eight deaths while Mohinder gains the resources to cure the disease that killed his sister, Shanti.
Matt Parkman, now divorced, has adopted a troubled Molly Walker with the help of Mohinder. Matt soon discovers that his father, also a telepath, is the "Nightmare Man" haunting Molly's dreams, and tries to track him down with Nathan Petrelli.
Niki Sanders temporarily leaves her son Micah in the care of her late husband's relatives in New Orleans while she goes to the Company, hoping to overcome her multiple personality disorder with their help. In the meantime, Micah discovers his cousin Monica Dawson has mimicking abilities.
New heroes Maya and Alejandro are introduced, each possessing a power; Maya produces a potent and lethal illness, while Alejandro's power is the antidote. They run from the law towards America, where they hope to find help from the author of the book Activating Evolution, Chandra Suresh, unaware that he is deceased. They pick up Sylar lying on the road (half-dead and powerless), who claims to know Suresh and says he can lead them to him.
