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.

A egotistical and super-charged Sylar goes to the Company to kill all the leaders, and inadvertently releases 12 super-powered criminals from the place's notorious Level 5 prison block during a fight with Elle. Peter, trapped in the body of one of the criminals, is set free as well and is forced to team up with a group for a crime spree. Meanwhile, Future Peter tries to fix his mistake with Nathan, as Angela takes over the company in the wake of Bob Bishop's murder and frees Noah Bennett to help the Company track down the 12 escapees and bring them back or eliminate them. In California, Claire learns more about her powers as she recovers from Sylar's attack. Hiro and Ando travel to Paris to track down speedster Daphne Milbrook who robbed them and learn that she is working for a darker power. In New York, Maya discovers that Mohinder's injection has changed him by making him super-strong, but also altered his personality. In Africa, Matt meats Usutu, an African shaman with a familiar power of painting the future. Elsewhere, Tracy learns that she has the power to super-freeze anyone and anything while dealing with a hounded tabloid reporter seeking any dirt on her and the shady Governor Maldon who are continuing to groom Peter for a position in the U.S. Congress.

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.

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.

Claire attempts to destroy her first target, Stephen Canfield. Hiro attempts to become friends with Daphne.

Fellow villains Knox and Daphne are sent by their emissary, Maury Parkman, on a quest to recruit Hiro and others to the Pinehearst fold. Adam Monroe is brought before the ringleader, who turns out to be the most powerful villain, who uses his power to heal. Matt Parkman arrives back in New York from his African adventure, and is confronted by Daphne with an offer to join their organization, but he instead wants a commitment from her. Hiro and Ando teleport to Africa to try to make contact with Usutu, the vision painter, for information on the persons behind all the recent events. Angela and the Company are paralyzed from recent events, and Noah Bennett is forced to team up with Sylar again to hunt down more escapees from Level 5. Peter goes to Pinehearst searching for answers, but is stunned to learn that his father, Arthur Petrelli, thought to be long dead, is the ringleader of the whole events, and who as the ability to physically absorb others powers by mere touch. Meanwhile, Claire and Sandra go on a mission to save Meredith from the clutches of Eric Doyle, a villain with abilities to control people mentally and physically. In New York, Nathan and Tracy try to trace their origins with Mohinder's help, but who has other plans for them.

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.

Under the guidance of Usutu, Hiro has a vision back in time one year ago to determine what forced Arthur Petrelli to fake his death and create Pinehearst. In the past, Hiro also watches the early days of the Company and how Mr. Petrelli and Mr. Linderman founded it, and their falling out with Angela who saw them as a threat to both Nathan and Peter. Also in the past, Meredith Gordon's origins are shown of how she was captured by Thompson to work for the Company, and of life of crime with her half-brother, whom is the blue-flame fire-starter Flint. Also, Sylar makes a discovery about his powers when he meets Elle for the first time and how she inspired him to kill in order to steal others powers.

Barely escaping from the evil and powerful Arthur Petrelli, Ando forces Hiro to teleport them back to Japan only to discover that Mr. Petrelli has erased most of Hiro's mind and who thinks he's 10-years-old, and still in school. Ando must try find a way to make Hiro remember his powers. Meanwhile, Sylar tries to reason with the captive Elle to force out her anger and to learn how to take her powers without killing her. Mr. Petrelli sends Knox and Flint out after Claire and Peter who try to find a way to outwit their pursuers. Matt Parkman tries to scan the comatose Angela Petrelli's mind to try to save her and learns that Daphne is a double-agent assigned to watch over him and that Mr. Petrelli has something against her. While Suresh continues to unsuccessfully search for the secret to the formula to give people powers, Nathan and Tracy pay a visit to Pinehurst where they meet with the manipulative Arthur Petrelli who offers Nathan the world in exchange for his loyalties and help. Nathan declines, but Tracy, eager to gain more power in politics, accepts.

Having reestablished control over the Company, Angela sends Nathan and Peter to Haiti to find the power-suppressing Haitian to bring him back to the USA to help in their fight against Arthur Petrelli and the evil Pinehurst. Hiro and Ando travel to New York to come back into the fold and ask for Parkman's help. Hiro, having lost part of his mind, but not his powers, teleports himself, Ando and Parkman to Kansas to Daphne's home to find out what Mr. Petrelli has on her. Also, Sylar teams up with Elle to try to capture Claire to bring her to Pinehurst to give her to Suresh to experiment on as the missing catalyst to the formula. But everything changes when a prolonged solar eclipse happens, which renders the heroes and villains powerless, stranding Peter and Nathan in Haiti with the Haitian who is trying to capture the powerful Voodoo witch-doctor Baron Samedi. In Kansas, Parkman must find a way into the Millbrook house without his mind-reading powers, and learns what Daphne is without her super-speed powers. In California, the powerless Elle and Sylar try to capture Claire, who accidentally gets shot, and Nathan seeks revenge.

In Haiti, Peter and the Haitian try to rescue Nathan who has been captured by the sinister Baron Samdei and his militia army. At Pinehurst, Mohinder finds himself a captive by Arthur who wants his powers back for a grand master plan, in which Mohinder attempts to find Maya to ask for help since she may be powerless too. In Kansas, Matt Parkman learns the true nature of Daphne without her super speed, while Ando and an immature Hiro seek answers to their powerlessness in a comic book store in the late Isaac Mendez's '9th Wonders' series detailing their conflict as it happens. In California, the powerless Claire is taken to the hospital dying from her wounds, while Sylar and Elle turn from hunters to the hunted when the vengeful Mr. Bennet attempts to track them down to kill them.

Having traveled back in time 16 years, the immature Hiro seeks out his late mother to try to get his memories back, while Claire has a run-in with a younger Noah Bennett when he was assigned by the company to look after the infant Claire and how she may have become the catalyst for the secret formula. Back in the present, Nathan returns to Pinehurst where Tracy introduces him to a group of U.S. Marines that Arthur has recruited to be his army of super-solders once Mohinder gets the catalyst for the ability-giving formula correct and which hopes the formula will be able to cure his disease... and begin Mr. Petrelli's quest for world domination. Peter and the Hatian return to New York and are sent by Angela in desperate attempt to break into Pinehurst to kill Arthur Petrelli before he can complete the formula. Meanwhile, Ando, Parkman, and Daphne seek out a bicycle messenger who may have the last '9th Wonders' comic book works to learn more about the future and where Hiro is and what to do to save him. Elsewhere, Sylar goes rogue once again by disposing of Elle, and then decides to go after both the heroes and villains to steal their powers for himself.

Noah, Claire, Angela, and Meredith find themselves trapped at the Primatech by Sylar who locks them in the building and subjects them all to various mind games. Meanwhile, Matt, Daphne, and Ando seek refuge at the Mendez loft where Daphne plans to steal a sample of the power-giving formula to give to Ando who wants to rescue the powerless Hiro still trapped 16 years in the past, who continues to struggle to find his true origins with his younger self. Back in the present, Peter faces off against Nathan, Tracy and the security detail at Pinehurst to stop Mohinder from reproducing the formula, and finds allies in the form of Knox as well as Flint who also want to stop the production of the formula, leading to a fiery showdown for all.

Two months after the destruction of both the Primatech and Pinehurst, and the death of Arthur Petrelli, the now-villainous Nathan returns with a vengeance by persuading the U.S. President and the government to round up all people with abilities for containment and disposal, leading to Claire, Ando, Peter, as well as Tracy to become fugitives from the people who were their former allies. In Japan, a powerless Hiro tries to live through the super-charger Ando as his latest partner. In New York, Peter struggles to find a life for himself as a paramedic, but finds that his cannot hide from his past. Claire learns about Nathan's and Angela's plans for interment of people with abilities and sets out to warn Matt Parkman who learns more about his abilities from the spirit of the African spiritualist Usutu. Elsewhere, Syler travels to Baltimore to locate his long-lost father and ends up being the only one who escapes from a government dragnet led by a mysterious agent known only as 'the Hunter'. Mohinder also learns that he has been targeted, and that Noah Bennett is apparently working with Nathan as well.

Following the plane crash, the surviving heroes must team up with one another to try to survive the manhunt. Claire is quickly captured by Noah who takes charge of a "kill squad" to find the remaining people with abilities while Nathan deals with the overzealous 'hunter' Emile Danko whom becomes obsessed with tracking down all people with special abilities in his own lethal way. Mohinder and a powerless Hiro must rely on Matt Parkman's spiritual guide to help them. Daphne makes contact with Ando to help her find Matt, unaware of the people now targeting them. In New Jersey, Syler takes refuge in the house of an agent and tortures him to try to get information to what's going on and he forms an unlikely alliance with the agent's son Luke Campbell. Also, Peter teams up with Tracy to look for help, while she begins having second thoughts about running.

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.

Peter, Matt, and Mohinder drug and abduct Noah "H.R.G." Bennet and hold him captive in a seedy motel room so Matt can interrogate him to find out more about the people hunting them down, but predictably, it does not go as planned as Benett plans to turn them against each other, while Nathan and the sadistic Danko are looking for him. Noah's background story is revealed about how Nathan approached him to help the government's plan to round up people with special powers, and his awkward alliance with Danko who has his own agenda... as does Nathan.

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.

The identity of "Rebel" is revealed with chilling consequences - Emmy Award-Winner Zeljko Ivanek, Brea Grant and Swoosie Kurtz Guest Star.

Denko is approached by Sylar with an offer to help him to find an elusive shape-shifting person, despite the fact that they don't trust each other. Meanwhile, Peter and Angela hide out in a church where she seeks a path of redemption from everything that she has allowed to happen to her, while Bennett is put in charge of finding both of them. In Mexico, Clare and Nathan hide out in a seedy motel where she takes advantage of her own abilities to win money in a drinking shot contest when they run short on money.

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.

Angela has nightmares. She gets the family to go back to Coyote Sands with her to dig up graves, and find her sister.

Sylar begins to feel confused and more uncertain about himself when his new shape-changing powers begins to get out of control. He begins to imagine his late mother giving him advice on what to do, while Danko continues to use him to find and kill people with abilities and wants to zero in on 'Rebel'. When Sylar discovers that Rebel is in fact Micah Sanders, he saves him. Sylar decides to change his ways after figuring out that Danko is plotting a so-called 'Final Solution' to exterminate all people with abilities once and for all. Meanwhile, Parkman plans to return to his home in California with his infant son unaware that there are more kill-squad agents after him, Hiro and Ando rashly decide to make a heroic, and probably futile, attempt to make an assault on Building 26.

Nathan and Peter try to find the shape-shifting Sylar before he can make contact with the President and assume his form as well. Clare goes off to try to stop Sylar on her own, only to end up as a captive. Meanwhile, Hiro and Ando make a rash attempt at stopping time so they can break into Building 26. They hope to free those that still survive and have powers, while Danko, framed by Sylar for the murder of an agent, has a talk with Noah Bennett over their views on fighting this war. Elsewhere, Angela meets with Matt to ask for his help to save Nathan, when she has a dream about him being in danger from Sylar.