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Season three opened with two one-hour episodes, airing on Monday, September 22, 2008 in the United States. The premiere of the third volume, "Villains", was preceded by a one-hour broadcast of the red carpet premiere, with clips from the past seasons and previews of the upcoming season, along with interviews with the series cast and crew. Volume Three began with the assassination attempt on Nathan Petrelli, and the consequences it has in the future. In addition, several villains escape from the confines of Level 5, and the Company attempts to recapture them. Arthur Petrelli awakens from a coma with the help of Adam Monroe’s healing abilities and eventually gains a few of the villains (Flint Gordon Jr., Knox, and Daphne Millbrook) while later luring in Mohinder Suresh, Nathan, Tracy Strauss , Elle Bishop, and Sylar. Their objective is to create a formula to give people abilities but after many failures they soon realize they need to find the catalyst. Claire and elementary-challanged Hiro go back in time with Hiro being given the catalyst by his mother. This is short-lived when Arthur intervenes and grabs the catalyst. Afterwards, Peter Petrelli, The Haitian face off Arthur at Pinehearst where they fight for control of the formula. In the end, Arthur is shot dead by Peter’s bullet through Sylar’s telekinesis ability, saying he is the killer not Peter. Peter injects himself with the formula in order to save Nathan, who was on his fathers side. Ando is given the ability to charge other peoples abilities (which helped him grab Hiro from the past with the help of Daphne’s super-speed ability); Claire, Noah Bennet, and Angela Petrelli fight off Sylar at Primatech in which Meredith’s ability goes awry burning the building to the ground with Sylar presumably dead.

"Villains" was originally designed to be included within the second season; however, because of the writers’ strike, the volume was carried over into season three. The lead-in to "Villains" showed Sylar regaining his lost powers, shown as the final scene of the "Generations" finale. Tim Kring said that the new volume would bring a cadre of villains to the show, hence the title. At the San Diego Comic-Con 2008 Kring screened the first part of the season opening episode of the "Villains" arc, entitled "The Second Coming", which was shown in its entirety at Comic-Con and received a positive response from fans. Despite the success of the first two seasons, Villains received steadily declining ratings and less positive reviews.

Volume Four begins with Nathan Petrelli telling the president about the existence of individuals who possess superhuman abilities. The president authorizes Nathan to capture heroes, and the majority of the main characters are rounded up, with the exception of Sylar, who escapes Nathan’s agents while attempting to locate his biological father.

The name of Volume Four was revealed by Tim Kring at the 2008 Edinburgh TV Festival. "Fugitives" will make up the last 12 episodes of Season 3 and air from February 2 to April 20, 2009.

Tim Molloy from TV Guide has reported that Heroes will return to its roots with "Fugitives" in an effort to attract new viewers and regain those who gave up on the show due to too many characters and plotlines. Tim Kring had said in a statement: "This volume starts us pretty much from scratch. There is almost nothing that the audience needs to know from the previous volume in order to follow the storyline." Molloy hopes the reboot will save the show from the declining ratings. Angela Bromstead, president of primetime entertainment at NBC, said the series was "very secure", but had not renewed it like The Office, 30 Rock, and The Biggest Loser. Bromstead had expressed her concern about whether the producers had strayed too far from its original focus: "ordinary people with extraordinary abilities," saying "They may have taken on too much in terms of characters and multiple storylines." The "Fugitives" story begins with the heroes trying to lead normal lives, until Claire discovers Nathan’s plot to hunt down and capture everyone with abilities, while Sylar begins searching for his biological parents.