Under the guidance of Usutu, Hiro has a vision back in time one year ago to determine what forced Arthur Petrelli to fake his death and create Pinehearst. In the past, Hiro also watches the early days of the Company and how Mr. Petrelli and Mr. Linderman founded it, and their falling out with Angela who saw them as a threat to both Nathan and Peter. Also in the past, Meredith Gordon's origins are shown of how she was captured by Thompson to work for the Company, and of life of crime with her half-brother, whom is the blue-flame fire-starter Flint. Also, Sylar makes a discovery about his powers when he meets Elle for the first time and how she inspired him to kill in order to steal others powers.

Having reestablished control over the Company, Angela sends Nathan and Peter to Haiti to find the power-suppressing Haitian to bring him back to the USA to help in their fight against Arthur Petrelli and the evil Pinehurst. Hiro and Ando travel to New York to come back into the fold and ask for Parkman's help. Hiro, having lost part of his mind, but not his powers, teleports himself, Ando and Parkman to Kansas to Daphne's home to find out what Mr. Petrelli has on her. Also, Sylar teams up with Elle to try to capture Claire to bring her to Pinehurst to give her to Suresh to experiment on as the missing catalyst to the formula. But everything changes when a prolonged solar eclipse happens, which renders the heroes and villains powerless, stranding Peter and Nathan in Haiti with the Haitian who is trying to capture the powerful Voodoo witch-doctor Baron Samedi. In Kansas, Parkman must find a way into the Millbrook house without his mind-reading powers, and learns what Daphne is without her super-speed powers. In California, the powerless Elle and Sylar try to capture Claire, who accidentally gets shot, and Nathan seeks revenge.

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.