Four months after the events of Peter's explosion, we find the heroes at different places in their lives. Claire, HRG and family try to stay below the radar in their new town, but a classmate of Claire's with some powers of his own knows there's something different about her. Matt Parkman and Mohinder Suresh are now guardians of Molly Parker, who has been suffering from horrible nightmares about the man who is more evil than Sylar. Mohinder and HRG are still trying to take the company down. Kaito Nakamura and Angela Petrelli receive ominous notices of their impending deaths, clearly sent by one of "the elders". Nathan has pushed his family away and is in a very dark place, feeling that Peter has survived and is alive somewhere. In Ireland, we find Peter Petrelli is alive, but doesn't remember who he is. Maya and Alejandro, two new characters, are wanted for murder due to her accidentally killing multiple people because of her ability to host a plague.

At the behest of his new employers, Dr. Suresh travels to Haiti to treat a potential virus victim. The patient turns out to be a familiar face. Claire's secret may be out when a fellow student sees her regenerate a limb; that student may have his own secret however. Matt Parkman investigates a murder that affects one one of the Heroes. In 17th century Japan, Hiro is doing his best to ensure that Takezo Sensei lives up to his reputation. He has to take things into his own hands however. In Ireland, Peter Petrelli finds himself with no memory but re-discovering some of his many powers. Maya and her brother reach the Guatemala-Mexico border in their quest to travel to the USA.

Now back from Haiti, Dr. Suresh finds that his new lab in New York is Isaac Mendez's old loft. He finds the 8th of Isaac's paintings but it holds bad news for a major character. Claire is concerned that her classmate will reveal her secret but he reveals a secret of his own. Peter Petrelli assists his newfound friends and begins to question whether he wants to know his identity and his past. Still in 17th century Japan, Hiro forces the issue with Takezo Kensei in order to ensure that he lives up to his legendary status. Niki Sanders travels to New Orleans to leave Micah with a relative. Maya and her brother reach Mexico, but she has to get him out of jail.

Micah warms his way into his cousin's heart by using his powers. Matt gets closer to finding some answers surrounding the mysterious mark on Hiro's father's photo and asks Molly to help him. Nathan's mother confesses to killing Hiro's father, and Claire grows closer to the classmate who can fly.

Having lied to her father about joining the cheerleaders, Claire decides the time has come to teach the team captain a lesson when she is told that she didn't make the squad. Having convinced Monica to come to New York, Dr. Suresh isn't at all comfortable when the Company asks him use her as a guinea pig for a variant of the vaccine. The Company backs down but he learns that Niki Sanders has been assigned to work with him. Alejandro and Maya make it to the US border only to be stopped by a citizens border patrol unit. Having painted a Menendez-like painting, Peter Petrelli heads for Montreal to see if they can get some clues as to who Peter really is. Hiro may ruin the time-line when he gives in to temptation and kisses Yaeko only to learn that Takezo Kensei was watching them. HRG man and the Haitian visit an old colleague from the Company in an attempt to locate Isaac Mendez's last paintings. They show that they are more than ready to use violence to get what they want.

In flashbacks, we learn what happened to the heroes in the four months after the events at Kirby Plaza. Maja learns of her deadly powers at her brother Alejandro's wedding. Niki starts a Company-sponsored drug program but stops taking the medication only to realize that another hidden personality has emerged. Imprisoned by the Company, Peter Petrelli meets the now familiar Adam Monroe and we learn how he ended up in the shipping container destined for Ireland.

Peter Petrelli and Adam Monroe track down another founding member of the Company and learn the location of virus 183. Maya learns how to control her powers but Alejandro' distrust of Sylar leads to a deadly confrontation. Niki returns to New Orleans and tells Micah about her medical condition. When his backpack is stolen, Micah and Monica set off to retrieve it, but things don't work out as planned. Hiro decides to avenge his father's death and goes after Adam. Claire, grieving over her father's death, decides to go public with her powers in a bid to stop the Company.

Nathan, Matt, and Hiro confront Peter and Adam at the Company's facility in Odessa, TX where Adam's intentions become apparent. Micah confides in his mother and working together; he and Niki set off to rescue Monica but with deadly results. Maya and Sylar visit Dr. Suresh and she finally realizes what Sylar is really up to. Noah Bennet visits his family and begs Claire not to publicly reveal her secret.

Under Samuel's guidance, Sylar starts on a path to rediscover his true identity. Hiro helps Emma accept and understand the great possibilities that go along with having an ability. Meanwhile, Peter enlists HRG to help him find a healer who can save Hiro's life.