Nathan tries to prevent Sylar from meeting the President. Sylar has his own agenda regarding his partner. Hiro finds there are consequences that come with the return of his powers.
Sylar, still engaged in an unlikely alliance, faces an identity crisis as his newest power begins to affect him in strange ways. Hiro and Ando try to bring down Building 26 as Matt grapples with fatherhood. Nathan begins to unfold a plan to to set things right.
Angela uncovers the dark secrets of her past, while Mohinder learns of his father's involvement in a forgotten government operation.
Someone close to Danko is put in the line of fire as he spearheads the anti-superhuman operation. Meanwhile, Noah's marriage continues to crumble while Hiro and Ando continue their journey to save Matt. Angela faces some demons from her past.
The heroes try to mend their broken relationships as Nathan and Claire seek refuge in Mexico and Peter and Angela hide out in a church. Danko's bid to wipe out the superpowered population intensifies as he unites with a surprising new ally.
The identity of "Rebel" is revealed. Noah wants Danko to let Tracy go in the hope that she will lead them to Rebel. Hiro and Ando continue with the mission that Rebel entrusted to them, to keep the new hero safe.
Sylar finds his father at last, Claire must decide whether to help a sworn enemy, Danko digs into the secrets of the Petrelli family, and Matt must find a way out of an explosive situation.
After a tip from "Rebel", Matt and Peter hurry to rescue Daphne and find evidence that may expose the government's plans to capture those with powers. Sylar uncovers the truth about his mother from past memories on his father, while the Hunter hatches an explosive plan of his own.
HRG and Matt are thrust into a series of mind games to uncover the truth about Nathan's plans. Peter gets to meet The Hunter in person.
As the President sends a representative to investigate Nathan's activities, Sylar continues his quest to find his father. Hiro and Ando travel to India to fulfill the destiny shown by Matt's drawing, and Claire risks her father's wrath to protect a new friend.
Our heroes truly become fugitives, and they are on the run from one of their own. Sylar begins the search for his father, and Matt's paintings reveal a dark fate.
After the battle between Pinehearst and Primatech, Pete, Claire, Matt, and Daphne try to live normal lives, while a powerless Hiro tries to teach Ando how to use his new special ability and become a superhero. However, Claire discovers Nathan's plan to track down those with abilities.
Nathan and Peter face off, and Nathan makes a move with far reaching consequences. Sylar takes desperate measures at Primatech and the fates of several heroes hang in the balance. Ando, Matt, and Daphne continue their quest to save Hiro.
Hiro and Claire unite in their bid to stop Arthur by traveling back in time. Peter and the Haitian go after Arthur and Sylar finds a way to discover once and for all about his lineage. Ando, Daphne and Matt search for the last 9th Wonders! story.
The eclipse continues to create chaos. Sylar and Elle face HRG's wrath. Peter, Nathan and the Haitian go up against Baron Samedi. Ando, Sam, and Frack try to help Hiro with his memory loss.
The eclipse plays havoc with the heroes' powers. Arthur orders Elle and Sylar to bring in Claire. Hiro, Ando, and Matt follow Daphne to her hometown to learn what hold Arthur has on her, and Peter and Nathan travel to the Haitian's hometown to recruit him for the war with Pinehearst.
Nathan learns of his father's plans while Flint and Knox launch attacks on Peter and Claire. Meanwhile, Matt tries to revive Angela, Sylar meets with Elle, and Mohinder begins testing of his newest superpower formula.
Hiro attempts to delve into Arthur Petrelli's past to uncover the mystery behind him creating a rival company Pinehearst and his hatred towards Angela. Sylar stricken by guilt tries to stop his murderous ways with HRG and Elle vying for his blood. Meredith's training goes up in smoke with the arrival of her brother.
Tracy and Nathan try to save themselves from a dangerous Mohinder who is no longer in control of himself. Sylar is given the task to save Peter from a rival company. Daphne is ordered to kill or be killed. Hiro is still searching for answers.
Villains Knox and Daphne are on a quest to recruit Hiro and others to the Pinehearst fold. Angela and the Company are paralyzed from recent events. Peter goes to Pinehearst searching for answers but is stunned to learn who the founder is. Claire and Sandra go on a mission to save Meredith from the clutches of Doyle, a villain with abilities to control people mentally and physically. Nathan and Tracy try to trace their origins with Mohinder's help.
Claire decides to take on one of the villains herself, but she may not be as invulnerable as she believes. Nathan and Tracy search for the truth about their origins. Maya makes a shocking discovery. Hiro and Ando look for help in the most unlikely places.
Peter travels to the future and adopts a dangerous ability in order to try to save the world. Meanwhile, Mohinder struggles with his continuing evolution from the formula, and Hiro and Ando re-unite with an old enemy.
HRG and his new partner go to a local bank heist with four villains; including Peter being trapped in one of them. Hiro and Ando track Daphne to Germany, and meet the Haitian. Tracy Strauss goes to New Orleans to find out more information about Niki. Meredith teaches Claire a lesson about fighting. Usutu shows Matt a series of paintings about him.
Sylar goes to the Company and inadvertently releases 12 super-powered criminals in a fight with Elle. Future Peter tries to fix his mistake. Angela takes over the company. Claire learns more about her powers. Hiro and Ando travel to Paris to track down the speedster who robbed them. Maya discovers that Mohinder's injection has changed him. Matt meats Usutu, an African with a familiar power.
After a look into the future, Nathan's shooter is revealed. Matt chases him and winds up in a desert. Hiro receives an important message from his father. Sylar visits Claire. Maya gives Mohinder an idea for his research. Nathan recovers and gets a visit from Linderman.
Before the third season premiere, a brief recap of Seasons 1 and 2 and interviews with the cast at the premiere party is shown.
