New York carer Peter Petrelli is having dreams of flying with his brother, politician Nathan. Peter helps one of his patient’s daughters (Simone) with her addict boyfriend Isaac Mendez. He has been unknowingly painting the future including the destruction of New York in a nuclear explosion. Indian geneticist Mohinder Suresh learns of his father’s death and suspects foul play. He heads to New York to continue his father’s work, looking for people carrying the genes which will carry the next step of human evolution. He is being followed by a man in spectacles who turns out to be the father of Texan cheerleader Claire Bennet. She has discovered she can regenerate her cells no matter what the injury. Meanwhile in Las Vegas, Niki Sanders is trying to avoid the mob who she borrowed money from to educate child prodigy Micah. She thinks she is losing her mind as her reflection seems to be coming to life and when it does she wakes up to find she has killed two men. Finally Japanese office worker Hiro tries to convince friend Ando that he can bend space and time. His experiments lead him to teleport to New York, just as Peter leaps off a building and discovers that he and Nathan can fly.
Peter wakes up in hospital and Nathan says it was a suicide attempt. His mother tells him that his father actually killed himself and suffered from depression. Claire asks her father if she can meet her birth parents. He says he is looking into it but he finds the video of her healing ability. Niki spaces out on the way to pick up Micah and finds that four hours have passed and she has cleaned up her garage and put the two men’s dead bodies in the trunk. There are also instructions on where to bury them in the desert. Mohinder is attacked in his apartment and begins to find answers with the help of his neighbour. Officer Matt Parkman in Los Angeles is helping out with a brutal murder. He begins to hear the voice of a girl who he finds hiding in the house where her family were killed. Finally Hiro finds a comic in New York detailing the last day’s events in his life. The comic was drawn by Isaac Mendez but when Hiro arrives at his loft, he has been murdered. The police call Ando who says Hiro has been missing for five weeks. A nuclear bomb goes off in New York so Hiro jumps back to the point where he left Japan.
Niki finds a ring in the grave she is digging. She heads to Micah’s Grandmother’s place and presents the ring as evidence of her husband DL’s guilt. Hiro convinces Ando to join him on his quest by following the steps laid out in the comic book. Parkman is enlisted by the FBI to help find Sylar, who survives a round of bullets and escapes while trying to abduct Molly. Mohinder finds Sylar’s apartment but when he returns with the police it is empty. Nathan announces that Peter tried to kill himself to the public. Peter quits his job and kisses Simone who left Isaac. Claire is killed by Brody while he is forcing himself on her and she wakes up while cut open on the autopsy table.
Claire escapes form her autopsy and goes home. She confronts Brody who is unrepentant and she drives them both into a wall at high speed. Hiro and Ando hit the casinos in Vegas and use Hiro’s power to win money. Niki is told to seduce Nathan to pay off her debt to Mr Linderman. She can’t do it but her alter ego does. Parkman wakes up in a lab run by Mr Bennet. Peter goes to see Mohinder and they travel together to see Isaac. Isaac is high and painting the future so they return home. On the way their subway freezes in time and Hiro from the future comes to give Peter a message.
Future Hiro tells Peter that saving the cheerleader will save the world. Mohinder doesn’t believe him and leaves. Peter heads to Isaac’s and finishes one of his paintings for him. Mr Bennet tries to abduct Nathan but he flies away. He meets Hiro in a diner before returning to the casino. Niki wakes up not remembering what happened but her debt with Linderman is cleared. She returns home to find Ando who came to see her. She is also told by the police that her husband DL is nearby. Claire tells her father what Brody did, so he has his friend take Brody’s memories. Parkman uses his powers to give his wife the best date possible, before talking down a robber and then collapsing again. Hiro and Ando get back together and call Isaac. Peter answers and is able to tell Hiro that he has a message for him.
Peter tells Hiro and Ando to come to New York. But as they head out they run into their friend with the cowboy hat again. He makes them play cards to pay him back for cheating but while they are in the bathroom their fellow players are all murdered (by Niki). DL and Niki make plans to be together again. He was set up by someone and escaped jail because he has the power to morph through solid objects. Niki realises that her alter ego set DL up and when he finds out he knocks her out and takes Micah and the money she stole. Claire meets her biological parents but they give her no clues as to why she can regenerate. But her mum does when she tells her that as a baby she had some kind of virus. Mohinder goes back to India and we learn that his neighbour Eden works for Mr Bennet. She is keeping an eye on Peter and Isaac as well.
Peter dreams of Simone’s father just as he dies. They go to see Isaac but he has gone. Nathan’s mum sets up a brunch with an influential journalist. He asks questions about Nathan’s trip to Vegas and Peter covers for him. Hiro rescues DL as he tries to rescue a woman from a burning car. Micah reveals his power by making an out of order phone work. He calls Niki and tells her where he is but she has allowed “Jessica” to take control. Parkman is enlisted by Agent Hanson again as she tracks Sylar. A dead oncologist leads them to Ted Sprague, a man emitting radiation from his body. Matt helps arrest him but then discovers that a colleague has been sleeping with his wife. Zach mysteriously finds the tape of Claire’s “accidents” and it falls into her brothers hands.
Mohinder considers forgetting all about his father’s work and going back to his normal life. But strange dreams reveal past events which change his mind. Parkman gets Sprague to open up about what happened to him. They discover they have both met the Haitian and have the same mark on their necks. Sprague escapes from custody just as Parkman confronts his wife about her adultery. Mr Bennet uses Eden to force Isaac to take heroin in order to paint more of the events which lead to Claire’s death. Hiro starts flirting with a waitress at a diner who can remember everything she reads. Sylar kills her and Hiro goes back in time to save her.
Mohinder finds the boy from his dreams. He has the power to visit people in their dreams and he says Mohinder already knows he must continue his father’s work. He then discovers his father’s list of all the people with special abilities. Claire becomes homecoming queen and punches a taunting Jackie. Isaac’s painting offers Mr Bennet no help so he grounds Claire. Zach helps her escape and she goes to the game. Simone sees the painting which Nathan bought from Linderman and tells Peter where to go. He arrives and manages to prevent Sylar from killing Claire, though he does kill Jackie. Peter survives as he has absorbed Claire’s healing ability. Sylar is captured by the Haitian and Eden. Ando waits in the coffee house as Hiro doesn’t return. Niki buys a sniper rifle while Micah convinces DL to try and help her.
As Hiro accidentally jumps back in time by six months, we see what all the other heroes were up to then. Hiro and Charlie fall in love but she tells him she is dying from a blood clot on the brain and he realises he can not change the past. Chandra Suresh is busy contacting the people on his list. He meets watchmaker Gabriel Gray who becomes Sylar when he works out how to look inside peoples brains to see how their powers work. He also contacts Mr Bennet and tells him about Claire. Mr Bennet captures Eden and asks her to make Chandra forget about Claire. We learn that Jessica was Niki’s sister and was killed by her estranged father. Meanwhile lawyer Nathan Petrelli is getting ready to lead a case against Mr Linderman which will expose his own father’s ties to the mob. But Linderman’s men run Nathan’s car off the road, paralysing his wife just as his power of flight kicks in. Finally Matt Parkman’s dyslexia costs him another detectives exam and his self pity begins to affect his marriage.
Parkman and Hanson interview Peter but the men both get splitting headaches as they hear each others thoughts. Parkman realises that the Haitian is near by and begins a stakeout of Mr Bennet’s work place. Inside they have isolated Sylar and received orders not to kill him. When Eden tries to kill him Sylar uses his powers to catch her but she kills herself. Meanwhile Mr Bennet sends the Haitian to take his wife, his son and Zach’s memories. Claire is freaked out by all this and the Haitian comes to her saying it is important that she remembers. Nathan bails out Peter who collapses in the street dreaming that he is the bomb that destroys New York. Meanwhile Eden helps Isaac escape and he meets up with Hiro and Ando who help him paint a picture of Hiro fighting a dinosaur. Although Jessica shoots DL through the shoulder, Niki finds them and apologises. Realising she is a threat to Micah she hands herself into the police.
It is two weeks later. Peter has been in a coma all that time. He has been reliving his dream over and over with now the addition of a bearded man laughing. He wakes up in hospital and heads out into the street planning to go into the desert so he can’t hurt anyone, but instead finds the bearded man who has the power of invisibility. Claire is pretending that she can’t remember anything. She takes Zach out to start filming her again so that she will not forget who she is. Hiro steals the sword of Takeshi Kensei but finds that the real one is with Mr Linderman. He goes to tell Isaac who has convinced Simone and Nathan that he can paint the future. Parkman fails to expose Mr Bennet’s workplace and confesses to his wife about his powers. Bennet heads off to ask Mohinder for help, but he refuses. Jessica keeps taking control of Niki and assaulting prison guards. DL gives Linderman back his money but is still in his debt.
Peter befriends the invisible man who agrees to help him control his powers. Claire asks the Haitian about her real parents. He gives her enough of a clue that she is able to track down her mother. Hiro and Ando are captured and taken to see Hiro’s father. Parkman is suspended for six months but gets good news when his wife tells him she is pregnant. Niki seeks psychiatric help while DL struggles to get a job. Micah uses his power to steal money from an ATM. Mr Bennet is told that Sylar is dead but when he arrives Sylar has outsmarted them all.
Claire meets her birth mother. Sylar is about to kill her actual mother when Mr Bennet and the Haitian save her. Claude the invisible man makes Peter steal, follow Simone and finally push him off a building to try and help him control his powers. Hiro’s father insists he come home as the shareholders of Yamagato industries have begun to question his ability to control his family. Hiro convinces him to groom his sister, not him, to be his successor. Isaac continuously paints the future and it helps him bond with Simone. It also allows him to see that Peter is invisible which he tells Mr Bennet. Jessica attacks the psychiatrist trying to help Niki but Mr Linderman arranges for all charges against her to be dropped.
Parkman is working as a bodyguard to Mr Malsky who has stolen two million dollars from Mr Linderman. Niki or rather Jessica has been hired to kill Malsky. She does and Parkman pockets the diamonds Malsky exchanged for the millions when the police treat his story with contempt. Claire’s biological mother extorts Nathan for money and she tells Claire that he doesn’t want to see her. Claire returns home to discover that her mother doesn’t remember who she is. Sylar tracks down another hero (Zane) and takes his power. When Mohinder arrives to see him, Sylar pretends to be Zane. Hiro and Ando return to Linderman’s casino but Ando gets sidetracked helping a girl called Hope.
Hiro and Ando escape with only a bullet in Ando’s shoulder from their casino crossfire. But Hiro sends Ando home as he believes he needs to be alone to complete the mission. Peter and Claude are caught by Bennet and the Haitian but escape when Peter remembers how to fly. Claude freaks out and leaves while Peter goes to accuse Isaac of selling him out. In their argument Isaac kills Simone. Mrs Bennet collapses and is taken to hospital. Claire tells her father that she knows about him and she is only staying to protect her family from him. Parkman is contacted by Ted Sprague who was contacted by new hero Hana Gitelman. They agree to track down Mr Bennet and stop him keeping tabs on them. Sylar and Mohinder visit a woman who has superhuman hearing and Sylar kills her and takes her power.
Sprague’s desire for revenge conflicts with Parkman’s desire to not hurt anyone. Mr Bennet and Parkman work together to try and avoid anyone dying but Thompson shoots Sprague causing him to go into meltdown. Claire tranquilises him, thus revealing her powers to Thompson. Mr Bennet pretends that the Haitian kept her powers from him and is left for dead with no memory of what happened.
Mr Bennet remembers nothing and sets off in search of Claire. But Mrs Bennet tells him that she remembers everything and they agree to let Claire go. She escapes from the Haitian and seeks out Peter Petrelli but instead meets her grandmother Angela Petrelli. A distraught Isaac is confronted by the police. Perception altering Janice arrives with Mr Bennet to smooth things over but she then betrays Bennet to the company. Isaac paints his own demise at Sylar’s hands. Mohinder discovers Sylar has been lying and drugs him. He uses Sylar’s spinal fluid to unravel his father’s formula. However Sylar recovers and captures him before the final scene when he tries to kill Peter Petrelli who came to look for Mohinder. Hiro gets a helping hand from Nathan and Ando in order to get Kensei’s sword and recover his powers. That done he jumps with Ando into the future where the bomb has gone off. Nathan is working with the FBI to take down Linderman but Jessica kills the agents accompanying him. Niki regains control long enough to give Nathan a gun to kill Linderman. But Linderman offers Nathan the Presidency and he doesn’t kill him.
Mr Bennet uses his thoughts to direct Parkman to help him and Sprague escape. He then tells them that they should head to New York to destroy the company’s tracking system. Sylar kills Peter but Mohinder escapes with his body and takes him to the Petrelli house. Claire helps revive Peter but Nathan tells her she needs to leave for a week so that he can win the election. Nathan returns from his meeting with Linderman with a picture of himself in the White House. Linderman takes Micah to help “save the world” while DL stands up to Jessica. Sylar heads to Isaac’s loft where he kills him. But Isaac tells him he painted how Sylar was killed and sent it somewhere. Hiro and Ando head to Isaac’s loft five years in the future but only find future Hiro.
Future Hiro is delighted to hear that Peter saved Claire. He now instructs Hiro to go back in time and kill Sylar. But the police arrive led by Parkman with the Haitian and capture our Hiro. Future Hiro and Ando seek out Peter who is with Niki in Vegas. The world believes Sylar exploded destroying New York. Since then Nathan has become President and tried to contain those with abilities by restricting their breeding. Mohinder has been unable to find a cure and so Nathan tells him he will kill all those with abilities in order to unite the world. Initially Peter won’t help Hiro, so he and Ando go to see Mr Bennet who is helping those with abilities to avoid detection. But he hands over Hiro to Parkman as part of a deal. Parkman is protecting his son Matthew while Bennet is hiding Claire’s location from the world. Parkman turns on Bennet and hands over Claire to Nathan. Nathan reveals himself as Sylar and takes her power. Mohinder kills the Haitian instead of our Hiro but future Hiro is killed by Parkman. Sylar reveals himself to Peter as Ando convinces Hiro to be a hero and go back in time to change all of this.
Having painted the future Sylar is worried that he is the bomb. He goes to visit his mother but his power disturbs her and he ends up killing her by accident. Hiro tries to kill him then but fails. Micah is being held by Candice at the Company’s New York office. Mohinder goes to work there and discovers a cure in his own blood for a disease which is killing Molly Walker. DL and Jessica go to Linderman’s and find files on their whole lives. Angela Petrelli tells Nathan that she has known about his powers all along and is involved in the plans for the future. Bennet, Sprague and Parkman arrive in New York and meet Claire and Peter. Peter absorbs Sprague’s power and struggles to control it.
Peter keeps his new power under control. He, Sprague and Claire agree to head far away, but Sylar is following them. He tips off the FBI who capture Sprague. Sylar takes his power. Micah fixes the election for Nathan and Linderman heals Heidi so she can walk. Hiro goes to get his sword fixed. He meets his father there who helps him train and tells him he was following him all along. Niki and DL kill Linderman who admits he arranged for them to meet to conceive Micah. Parkman and Bennet arrive at Molly’s room to kill her but Mohinder won’t let them.
Parkman, Bennet and Mohinder all agree not to hurt Molly. Hiro takes Ando back to Japan to keep him safe. Sylar paints his final showdown with Peter at Kirby Plaza so he heads there. Peter seeks out Nathan’s help but he and Angela take Claire away. She escapes by jumping out of a window. Peter begins going radioactive and blacks out. He has a vision of Charles Deveaux and Angela discussing the bomb and her true opinion of Peter. Bennet wakes him up and they go to confront Sylar. Niki realises she has the same strength as Jessica and knocks out Candice and rescues Micah. All our heroes meet in Kirby Plaza and help distract Sylar long enough for Hiro to arrive and stab him with his sword. Sylar sends him flying away and he jumps into the past by accident. Peter can’t stop going nuclear but before Claire is forced to kill him Nathan arrives. He flies Peter high into the sky so that he can explode where no one will be hurt.