Season one featured 23 episodes, which aired on Mondays at 9:00 pm in the United States, beginning on September 23, 2006. Season one consisted of Volume One, known as "Genesis". The series went on hiatus twice; first from December 4, 2006 to January 22, 2007, and again from March 5 to April 23, 2007, with the season finale airing on May 21, 2007. The volume begins as a seemingly ordinary group of people gradually become aware that they have special abilities. Events illustrate their reactions to these powers, and how the discovery affects their personal and professional lives. At the same time, several ordinary individuals are investigating the origins and extent of these abilities. Mohinder Suresh, a geneticist, continues his late father's research into the biological source of the change, while Noah Bennet represents a secret organization known only as the "Company". While coping with these new abilities, each of the characters is drawn, willingly or unwillingly, into the Company's conspiracy to control superpowered people and into a race to stop an explosion from destroying New York City.

Season two featured 11 out of a planned 24 episodes which aired on Mondays at 9:00 pm in the United States beginning on September 24, 2007. Only 11 out of the planned 24 episodes were broadcast due to the WGA writers' strike. Season two consisted of the second volume in the series, titled "Generations". Season two ended with its finale on December 3, 2007. Volume two begins four months after the events of Kirby Plaza. The main plot arc of "Generations" deals with the Company and its research on the Shanti virus. This research is explored through the Company's founders, whose identities are revealed, as well as through the effects of various strains of the virus. The "heroes" ultimately come together in an attempt to stop the release of a deadly strain of the virus and avert a global pandemic. Season 2 was originally going to comprise three volumes, however due to the writer's strike, the season was redesigned to only encompass one volume called "Generations". Originally Volume 3 was going to be called "Exodus", and Volume 4 was going to be called "Villains". As a result of the writers' strike, Volume 3 was changed to "Villains" and moved into season three. The "Exodus" story arc, which was originally designed to be a story arc reflecting the effects of the release of strain 138 of the Shanti virus, was canceled. Scenes from the volume two finale "Powerless", were reshot to reflect the cancellation of the "Exodus" volume, and to tie-up all the loose plot storylines of "Generations."

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. "Villains" was originally designed to be included within the second season; however, due to 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 has said that the new volume will bring a cadre of villains to the show, hence the title. On December 5, 2007, at the Jules Verne Film Festival Adventure, Tim Kring showed a video-preview of volume three. According to an interview with Allan Arkush, filming for season three began on May 1, 2008. On May 9, 2008, a season three promo clip was released with hints at possible "inner villains" within the heroes. The promo stated, "In every hero there could be a villain," before plastering the words "hero" and "villain" over the face of every major character. Finally, during the featured Heroes panel at the San Diego Comic-Con, the entire first hour of the first episode of the "Villains" arc was shown. In July NBC began airing a teaser for season three featuring Noah Bennet talking to Claire stating, "Since before you were even born, I was finding these people and locking them away so that they couldn't hurt anybody. Now a dozen of them have escaped, and they will kill...and they will terrorize...and they will conspire...and they will cause...unimaginable destruction to the world...they're villains, Claire," while a montage of clips play. Zachary Quinto, who plays Sylar, has stated that the Villains story arc will last for thirteen episodes. 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. The name of Volume Four was revealed by Heroes creator Tim Kring at the 2008 Edinburgh TV Festival. "Fugitives" will make up the last 12 episodes of Season 3.