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.

Afraid of losing the love he thinks he's found, Peter denies his past and doesn't look in the box while an unknown woman tries to track him down. Parkman and Nathan are led to Philadelphia to track down Matt's father, unknowingly being led into a trap where Nathan stumbles into the city that blew up after all. Mohindar takes Molly to the Company in search of help for her, just as Nikki shows up, while another hero begins to discover her powers in Texas.

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.

Peter Petrelli finds himself in a future New York City where a virus has devastated the world's population. As he gradually regains him memory, he recognizes his mother who urges him to use his Hiro-like powers to go back in time and stop the virus before it begins. Claire and West's relationship reaches a crisis point when West realizes that her father is the same man who once kidnapped him. Suresh's loyalty to HRG man is starting to wear thin and he finally admits what he has been up to. Nathan learns that brother Peter is alive. Matt Parkman finally confronts his father in an attempt to release Molly from her coma-like state. Having fallen out completely with Takezo Kensei, Hiro attacks White Beard's camp. A new character with a familiar face, Adam Monroe, is revealed as one of the founders of the company.

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.