Five Years Gone

This episode focuses on Hiro Nakamura and Ando Masahashi traveling five years into the future, showing where the world will be if the explosion isn't stopped. Future Hiro, last encountered in the episode "Hiros", is featured more prominently, this time as the world's most wanted terrorist and a master of Battōjutsu. Ando was killed in the blast, which according to Peter, is the reason why Hiro lost his humorous side and became obsessed with changing the past.

Nathan Petrelli is now the President of the United States, with Mohinder Suresh as his Chief Medical Advisor and Matt Parkman as the head of Homeland Security with the Haitian at his side. Niki Sanders has become a stripper again, adopting "Jessica", the name of both her former alter ego and sister, as her stage name. Her son Micah was killed in the explosion that destroyed much of New York. Niki has a romantic relationship with Peter Petrelli, who has a distinct scar across his face which starts on the right side of his forehead down to his left cheek.

Sylar is blamed for detonating a nuclear explosion that destroys half of New York and kills millions of people, and is assumed to be deceased. In the original timeline, Hiro had stabbed him before the explosion, but Sylar had already succeeded in killing Claire Bennet at her high school Homecoming, absorbed her regenerative powers, and survived. However, this timeline was altered and did not actually occur, as Hiro had visited Peter Petrelli with the message "save the cheerleader, save the world" and, consequently, Sylar was denied the ability of spontaneous regeneration. Nonetheless, the explosion did occur and, in reality, Peter was the cause of the blast in the alternative timeline. Nathan lied to the public to protect his brother, and blamed Sylar for the explosion.

Sylar was able to kill Nathan and impersonate him after killing Candice and acquiring her illusory ability. For him, the hunting and, eventually, extermination of other superpowered people is all part of his "eliminating the competition".

With Sylar disguising himself as Nathan, acting as President (reminiscent of Isaac Mendez' painting), and exploiting public panic after the destruction of New York, persons with special abilities are now viewed with fear and suspicion and are subject to heavy persecution, with the Department of Homeland Security (including Parkman and the Haitian) working to hunt down "unregistered" individuals in accordance with the "Linderman Act". Mr. Bennet and Hana Gitelman work to hide heroes and their families, giving them new identities and moving them to keep them safe. Mr. Bennet has made a secret bargain with Parkman, however, to turn over individuals with "dangerous" powers, while Parkman allows Mr. Bennet to continue helping others with "harmless" powers, including Parkman's own wife and son.

One of the individuals Mr. Bennet is hiding is his adopted daughter Claire. She becomes a brunette and goes undercover as a waitress in Midland, Texas at the Burnt Toast Diner, the same place Charlie Andrews worked at, using her adoptive mother's name, Sandra. Parkman betrays Mr. Bennet after finding out that there are indeed two Hiros and one of them escaped him. Not wanting to face the President empty-handed, he extracts Claire's location from Mr. Bennet's mind, and then shoots his former ally (Hana Gitelman was also killed prior to the confrontation between Parkman and Bennet). Parkman proceeds to capture Claire, who was about to go on the run, and sends her to the Petrelli mansion in Manhattan. There Sylar, under the guise of Nathan, attacks her and once again obtains her power in this alternative timeline.

Meanwhile, present-day Hiro has been captured by Parkman. When Nathan orders Mohinder to kill Hiro to begin his plan of genocide of the super-powered, Mohinder instead kills the Haitian and allows present-day Hiro to escape. Mohinder then shows present-day Hiro a new copy of Isaac Mendez's 9th Wonders! comic book (the same copy Isaac drew before being murdered in the previous episode), where Mohinder is shown injecting the Haitian.

When Peter, Future Hiro and Ando stage an attack to free present-day Hiro, Parkman calls the President to inform him that they're being repelled by Peter. Upon hearing this, Sylar, still disguised as Nathan, flies away in front of a crowd to whom he just gave a speech about the last five years, effectively revealing to them that he too is a super-powered individual. Sylar reveals himself to Peter and they prepare to battle. Peter generates fire with his hands, while Sylar surrounds his with ice.

When Mohinder demands that present-day Hiro go back to the past, the less-experienced Hiro states that he doesn't know how to get back to the correct date. Before Future Hiro can take his earlier self back in time himself, he is shot in the back by Parkman. As Future Hiro dies, he gives Ando a page of Isaac's comic book. As present-day Hiro expresses his shock at seeing his own death, Mohinder pushes Future Hiro's katana into his hands and tells him to go quickly. Hiro and Ando travel back to the past and look happily upon the undestroyed city before them. Hiro looks at the comic strip of him killing Sylar and says, "Now, the hard part".