When Nikki wakes up, she sees the two criminals dead in her garage. She brings her son and finds a brand new Cadillac in her name and the bodies in the trunk, with instructions and a map to bury the corpses in the desert. Peter awakes in the hospital and his mother tells him that his father was depressed and committed suicide. When Peter decides to jump from the terrace of his building, his brother Nathan discloses that both can fly. Hiro is teleported to the Times Square and finds a comic book written by Isaac Mendez telling his saga. He goes to Isaac studio, finds him dead and is arrested by the police. A man pretending to be an exterminator bugs Mohinder's apartment, but he fights with the guy and is helped by his next door neighbor. In Los Angeles, the Police Officer Matt Parkman telepathically hears the voice of a child in a murder scene and is arrested as a suspect. Claire hides her heroic rescue in the fire and her seemingly evil adoptive father discloses her abilities in her stolen tape.

As the "Heroes" continue to test their newfound extraordinary abilities, Claire tries to maintain a normal social life when a romance with the football quarterback takes a tragic turn. While Hiro convinces his friend that they are destined to travel to America to save the world, a frightened Niki follows instructions from a mysterious, unknown source that directs her to the middle of the desert. Meanwhile, Nathan uses Peter's accident to propel his political campaign. The elusive Sylar is being hunted by both Matt and the FBI, as well as Suresh, whose father's journal leads to potential clues.

As Nathan and his family ready for the election, Hiro and Ando face the hard part of saving the world.

Peter feels the need to control his newly absorbed power, as he overhears Sylar's thoughts on the streets of New York. Mohinder finds another hero and agrees to help find a cure for her fatal disease, as Parkman and Bennet close in on the building they are in, looking for a link that could set them free. Niki/Jessica and D.L. are convinced that Linderman is behind their son's disappearance, as Linderman convinces their son to do a job for him.

Can Sylar be stopped? Will Linderman's vision live on with Nathan? What will it take for Peter to save the world, what sacrifices will be made? With all the horrible predictions unfolding before them the heroes face moments of pain and peril in Kirby Plaza.

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.

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.

Hiro learns of his father's death and travels back in time to save him only to realize that he must let events unfold as fate intended. He does however recognize his father's killer. Matt Parkman realizes that he has the ability to implant thoughts in other people's minds. He wants to know the identity of the woman in the photo with his father. When Bob and Suresh kidnap Claire Bennet, HRG and West set out to rescue her but get their own bargaining chip beforehand.

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.

Having time-traveled four years in the future, the future Peter shows his younger counterpart that people have access to drugs that give them various super powers and some of them will destroy the world. Past Peter is forced to run from the dark and evil future versions of Claire, Daphne, and Knox, all of whom work as killers for government agencies to track him down. Past Peter is forced to look for allies and finds one in a very subdued version of Sylar. From his spot in Africa, Matt Parkman has a vision of his future in four years in which he is married to Speedster Daphne and is still looking after Molly Walker whom also works for the agencies. In the present, Hiro and Ando are locked away in a Level 2 prison cell where their situation starts to drive a riff between them. Tracy learns more about her origins from Dr. Zimmerman, and Nathan receives more tips from the ghost of Mr. Linderman over his position for congress. Also, Mohinder learns that the powers he gave to himself are irreversible and could lead to disaster.