Noah, Claire, Angela, and Meredith find themselves trapped at the Primatech by Sylar who locks them in the building and subjects them all to various mind games. Meanwhile, Matt, Daphne, and Ando seek refuge at the Mendez loft where Daphne plans to steal a sample of the power-giving formula to give to Ando who wants to rescue the powerless Hiro still trapped 16 years in the past, who continues to struggle to find his true origins with his younger self. Back in the present, Peter faces off against Nathan, Tracy and the security detail at Pinehurst to stop Mohinder from reproducing the formula, and finds allies in the form of Knox as well as Flint who also want to stop the production of the formula, leading to a fiery showdown for all.

Two months after the destruction of both the Primatech and Pinehurst, 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 for containment and disposal, leading to Claire, Ando, Peter, as well as Tracy to become fugitives from the people who were their former allies. In Japan, a powerless Hiro tries to live through the super-charger Ando as his latest partner. In New York, Peter struggles to find a life for himself as a paramedic, but finds that his cannot hide from his past. Claire learns about Nathan's and Angela's plans for interment of people with abilities and sets out to warn Matt Parkman who learns more about his abilities from the spirit of the African spiritualist Usutu. Elsewhere, Syler travels to Baltimore to locate his long-lost father and ends up being the only one who escapes from a government dragnet led by a mysterious agent known only as 'the Hunter'. Mohinder also learns that he has been targeted, and that Noah Bennett is apparently working with Nathan as well.