Nathan's shooter is revealed. Elsewhere, Sylar visits Claire; Hiro and Ando guard a dangerous family secret and fret over the bleak future involving a dubious woman (Brea Grant); and Suresh makes an important breakthrough.
Angela confronts Peter; Sylar attacks the Company's main facility; Claire has a revelation about her powers; a group of dangerous criminals escape during a battle with Elle; Hiro and Ando follow Daphne to Paris; Matt seeks help from a guide (Ntare Mwine); Suresh is pleased with the recent developments in his life.
Angela recruits Noah Bennet and his new partner to diffuse a hostage situation at a bank; Peter tries to blend in while trapped inside an escapee's body; Hiro and Ando have a run-in with the Haitian; and Claire seeks advice from Meredith.
Claire hunts a Level 5 escapee who can create black holes; Linderman asks Daphne to recruit Hiro, who has trouble wrangling Adam; Maya discovers Suresh's transformation; Nathan helps Tracy find answers; and Peter's violent urges escalate.
Knox and Daphne give Hiro a mission to find the precog; Claire and Sandra plan to rescue Meredith; Nathan and Tracy seek help from Suresh to find the origin of their abilities; and Sylar and Peter look for the cause of Angela's vegetative state.
Hiro follows Arthur in the past to uncover what drove him to create Pinehearst; Meredith's brother disrupts her new life and training under the tutelage of Thompson (Eric Roberts); and Elle and Noah's persistence prevents Sylar from stopping his quest.
Arthur sends Knox and Flint after Peter and Claire; Nathan learns the truth about his father; Sylar confronts Elle at Pinehurst; Suresh experiments with his new formula; and Matt tries to revive Angela.
Part 1 of 2. Arthur sends Sylar and Elle after Claire; Matt, Hiro and Ando follow Daphne to uncover her secret; Nathan and Peter search for the Haitian in hopes that he can stop their father. Seth Green and Breckin Meyer guest star.
Conclusion. Elle and Sylar face Noah, who's out for revenge; Peter and Nathan help the Haitian with his brother (Demetrius Grosse); and Ando, Sam and Frack try to restore Hiro's memory using a comic book.
Hiro and Claire go back in time to the moment Noah took Claire from Kaito Nakamura; Sylar interferes with Peter and the Haitian's attempt to defeat Arthur; and Suresh makes major progress with the formula.
The newly powerless Hiro resolves to help Ando become a true superhero. Elsewhere, Suresh, Peter, Daphne and Matt return to their regular lives, but Claire's quest for normalcy is cut short after she discovers a new plot by Nathan; and Sylar looks for his real parents.
Matt's paintings reveal a dire fate for someone close to him; Sylar meets a young outcast (Dan Byrd) with abilities who may be able to help Sylar find his dad; and Nathan's new quest has people with abilities on the run.
Nathan becomes the focus of an investigation by Homeland Security. Meanwhile, Nathan's agents hunt for Sylar and Luke, who take a road trip to find Sylar's father; Claire tries to protect a man her dad is targeting; and Hiro and Ando go to India, led by Matt's prophetic images.
Matt and Peter go to Building 26 to locate Daphne and the files detailing the government's plans for people with abilities; Claire receives unexpected help getting Alex out of the city; Sylar uncovers memories of his father that reveal info about his mom; and the Hunter pursues his own agenda.
Sylar finally meets his father (John Glover) during an unusual reunion; Claire considers helping Doyle evade capture, despite their bitter past; the Hunter tries to expose Petrelli family secrets in hopes of usurping Nathan's operation; and Matt garners attention.
Nathan and Claire hide out in Mexico after Nathan's ability is exposed. Elsewhere, Danko enacts his plan to destroy those with abilities, with help from an unlikely source; and Angela and Peter make strides toward forgiveness while holed up in a church.
Sylar has an identity crisis while working with his partner; Hiro and Ando plot to destroy Building 26; fatherhood shifts Matt's perspective; and Nathan plans to repair the damage caused by his former operation.
Nathan takes on Sylar in order to shield the president in the third-season finale. Elsewhere, Hiro discovers unexpected side effects from recovering his ability, and Matt takes extreme measures to protect his family.