Five years in the future …
Future Hiro has taken up arts and crafts in the name of history. Future Peter has a nasty scar across his face, and has taken up with Future Niki, who is stripping again. There is no Future Jessica, Future Micah is dead, and Future D.L. is in the Hero Protection Program, which is run by Future Bennet, who along with Future Hana is hiding Future Claire, who is a brunette waitress in Future Texas and is getting married soon. Future Matt and Future Haitian are fascist asshats. Future Ando is dead. Future Mohinder works for Future Nathan, who is President, but who is really Future Sylar using Dead Candice’s shapeshifting power.
Future New York City has looked better. According to Future Hiro, Sylar was the bomb that exploded five years ago. But according to Future Peter, HE was the bomb, and Nathan/Sylar has been protecting him all this time. Regardless, Future Hiro had hoped to prevent this outcome entirely by going to back to that subway car to tell Peter to “Save The Cheerleader” — one of two critical points in hero history. Future Hiro’s reasoning is that he had an opportunity to kill Sylar just before the “the bomb” went off, but couldn’t, because in that timeline, Sylar possessed Claire’s healing ability and couldn’t be killed. So Sylar — who had killed Candice at some point — blew up NYC, took Nathan’s identity, and went on to become President. (It’s not established when or how Nathan died.) President Sylar has since created a police state built on fear, where anybody with powers is considered an outlaw and/or terrorist.
Regular Hiro and Regular Ando arrive in the future on the fifth anniversary of the explosion. They hook up with Future Hiro, Regular Hiro gets captured by Future Matt, and long story short, Future Peter and Future Hiro kick some ass and help Regular Ando get back together with Regular Hiro. Future Mohinder follows the cue given him in Dead Isaac’s final comic book — along with some gut instincts — and decides to betray President Sylar’s orders, knocking out Future Haitian, and giving Regular Hiro and Regular Ando the opportunity to escape back to Regular New York. Regular Hiro knows now that he has to kill Sylar, not only to save the world, but to save his best friend Ando, without whom he will completely lose his sense of humor.