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.

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.

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 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.