In Manhattan, Peter Petrelli is the younger brother Nathan Petrelli an overly ambitious and unscrupulous candidate for the next New York congressman, and he dreams and believes that he can fly. He decides to prove his theory and jumps from the roof of a building in an alley and his brother flies and saves him. In Texas, cheerleader Claire Bennet learns that she is literally indestructible and can not harm herself or die. She saves a fireman in a fire in a train, but does not take the credit. In Tokyo, Hiro Nakamura believes he can control time and space continuum. In India, Mohinder Suresh moves to the Brooklyn, New York, where his father, that was researching a secret project called Genesis about genome and DNA, is killed in a taxi cab. In Lower Manhattan, the painter Isaac Mendez paints pictures of the future. In Las Vegas, stripper Niki Sanders borrows $30,000 from a powerful local mobster to get her young son into school, and does not have the money to pay her loan. She sees a different image of her in the mirror, and when two gangsters come to her house to collect the money, one of them hits her and she faints. Later Nikki wakes up, and the two thugs are dead... literally torn apart by her evil alter ego.

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.

Suresh finally tracks down one of his father's fabled genetically advanced "supermen." In Las Vegas, Hiro's plan backfires when he cautiously turns time to his advantage at the gambling tables. Niki's mafia debtors use their leverage to their benefit in a more elaborate scheme, while Nathan pays a personal visit to a wealthy Vegas contributor to raise additional campaign funds. Following a tragic turn at a bonfire, Claire's uncanny healing abilities are put to the ultimate test, but according to Isaac's paintings, her future could be fraught with even more peril. Meanwhile, Matt's abilities are gauged by a pair of men who seem to know a great deal about people with special gifts.

Lyle Bennett learns of his sister Claire's secret after watching her video of her trying to kill herself. Hiro Nakamura helps D.L. Hawkins save a woman from a burning car by freezing time. Isaac Mendez has gone M.I.A. with his painting.

The question on everyone's mind regarding the cheerleader is that, since she's still alive, does the bomb still go off? This is especially true for Hiro, who meets with Isaac to discuss their next course of action. Having confessed her abilities to her father, Claire seeks other answers that her friends and family can not give. Having captured Sylar, Claire's father keeps him in a room of total darkness, totally unaware of Sylar's true strength.

Peter painfully learns that someone close may have betrayed him and Claude. Matt's world spirals out of control when radioactive man Ted Sprague and Hana Gitelman, a fierce young woman with "wireless" mental abilities, drop into his life. After blood is spilled, Hiro makes a difficult decision about his mission. Claire is unable to contain her anger at her father.

H.R.G.'s past catches up to him as Matt and Ted Sprague come to Texas looking for answers, and take him, his wife, son and Claire hostage -- leading to a tragic, explosive showdown.

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.

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.

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.

In order to change the course of history, a scared and cynical Peter Petrelli travels back in time from four years to the day his brother Nathan revealed the existence of the super-humans and was the one who shot him. In attempting to capture future Peter, Matt Parkman gets teleported to a desolate African landscape. In Japan, Hiro takes control of his father's company when, courtesy of a DVD, he and Ando receive instructions from Hiro's late father about a deadly secret contained in the office safe. Hiro can't help but open the safe and the contents are promptly stolen by a "speedster"; a woman with super-fast speed called Daphne. Meanwhile, Nathan undergoes a religious experience while recovering from the shooting and is offered a new job in Congress by a shady blond government woman named Tracy Strauss, someone who looks remarkably like the late Niki Sanders. Elsewhere, Sylar confronts Claire, whose alone in her house, in a bid to get hold of her powers.

Noah Bennett is stunned when Angela Petrelli assigns him a brainwashed Sylar as his new partner to track down the escapees from the notorious Level 5, as Peter, still trapped in the body of Jesse the Sonic Man, is forced to team up with a trio of deadly super villains who are on a murderous crime spree by holding up a local bank. Future Peter eventually releases Present Peter from his body-cell and shows him his dark future. In Africa, Matt learns more about his spiritual guide, Usutu, who also has the ability to paint the future. Meanwhile, Hiro and Ando track Speedster Daphne to Berlin to recover the mysterious formula, and find out that the rouge Haitian is behind it and working for another third party. In California, Claire asks her biological mother, Meredith Gordon, to teach her how to fight. Elsewhere, Micah Sanders, mourning the death of his mother is approached by the shadowy Tracy Strauss who asks him information about her past and why she and the late Niki Sanders are very identical looking, which leads to the mysterious Dr. Zimmerman, who may hold a clue.

Tracy and Nathan try to save themselves from a dangerous Mohinder who wants to use their synthetic power laced DNA to find a way to remove Mayas/his own powers. Mohinder turns to the dangerous, power-stealing Arthur Petrelli to help Maya, and in return, Mr. Petrelli asks for Mohinder's help in developing the secret formula to give people powers. Meanwhile, Sylar is given the task by the comatose Angela to save Peter from Arthur at Pinehearst, where he was captured and rendered powerless by his him. Also, Daphne is ordered by Mr. Petrelli to kill Matt, but finds the task difficult as she begins falling in love with him as he predicted. In Africa, Hiro is still searching for answers from the spiritual painter about who is behind Pinehearst and what their nefarious plans are for the world. In California, Elle approaches Claire and asks for her help to control her powers which leads to both of them forming an uneven alliance to venture to Pinehearst in New Jersey to find answers. Also, H.R.G. recruits Meredith as his new sidekick to track down more Level 5 escapees.

Imprisoned inside the super-secret 'Building 26' which is Nathan's base of operations to experiment and terminate people with abilities, Tracy struggles to survive various "heat" experiments as well as wait for an opportunity to try to escape. While the ruthless Hunter Davko obsessively continues to track down the heroes with the obsession of killing them all, Nathan deals with the President of the USA who begins to investigate Nathan's activities and tactics to hunt down the "targets". Meanwhile, Syler continues his quest to locate his biological father with both help and inference from Luke Campbell, as well as government agents now after both of them. Hiro, Ando, and Matt travel to India to find a new ally with abilities to help them survive. In California, Claire faces the wrath of her father.

Following a tip from their anonymous source "Rebel", Matt and Peter hurry to rescue Daphne from the holding facilities in 'Building 26' in Washington, and to find evidence that may expose the government's plans to capture those with powers. Meanwhile, Sylar uncovers the truth about his mother after he experiences past memories of his father at a disused diner located deep in the New Mexico desert which makes him dump Luke and head off to look for his biological father. In California, Claire must find a way to sneak Alex out of her house which is under observation by FBI Agents, and Mrs. Bennet reluctantly agrees to help. Elsewhere, Danko hatches another nefarious and explosive plan of his own to trap and kill Matt. Also, Claire has a run-in with an old villain, Eric Doyle, whom she captured a while back who asks for her help to hide from government assassins after him too.

Now on his own, Sylar finally finds his biological father, Samson Gray, a reclusive, lung-cancer ridden taxidermist, to confront him with questions about his past, but soon learns that Samson is not who he appears to be. Meanwhile, Nathan continues to lock horns with Danko over the hunter's tactics to eliminate people with abilities, after he tries to frame Parkman for an attempted suicide bombing. This leads to both Nathan and Danko going behind each others back to unseat the other. Nathan becomes wary about Danko going rogue and the hunter interrogating Tracy, as well as Nathan's mother, Angela, about Nathan's own ability. In California, Claire takes Alex's old job at the comic book store where she is given a message by 'Rebel' to help out her former nemesis, the puppet master Eric Doyle, when he too is targeted by rogue agents. Also, Hiro and Ando return to California where they are led by clue from Rebel... to an infant Matt Parkman.

Hiro and Ando set out to find Matt Parkman with his infant son, but soon learn that the infant's powers hinder their travel plans. Meanwhile, the shape shifting Sylar begins to use his new powers to harass Bennet by impersonating his wife, Sandra, knowing he will find out. An angry Matt Parkman begins investigating the sadistic Danko to see revenge for Daphne's death and learns more about his pursuer when he meets his Slavic girlfriend Alena. Mohinder learns more about his father's work about a mysterious place called Coyote Sands in which Angela and Peter make contact with Nathan and Clare where Angela takes them to the remote location where a secret about Angela's past lies buried.