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.

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.

In flashbacks, we learn what happened to the heroes in the four months after the events at Kirby Plaza. Maja learns of her deadly powers at her brother Alejandro's wedding. Niki starts a Company-sponsored drug program but stops taking the medication only to realize that another hidden personality has emerged. Imprisoned by the Company, Peter Petrelli meets the now familiar Adam Monroe and we learn how he ended up in the shipping container destined for Ireland.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

In flashbacks, we learn what happened to the heroes in the four months after the events at Kirby Plaza. Maja learns of her deadly powers at her brother Alejandro's wedding. Niki starts a Company-sponsored drug program but stops taking the medication only to realize that another hidden personality has emerged. Imprisoned by the Company, Peter Petrelli meets the now familiar Adam Monroe and we learn how he ended up in the shipping container destined for Ireland.

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.

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.