Set directly after Stargate Atlantis Season 5, the series begins with the Atlantis expedition coming to terms with the IOA's desire to keep Atlantis for the protection of Earth. However, thanks to the efforts of General Jack O'Neill, the IOA relents and chooses to let Atlantis go rather than see it fall into the possession of the United States.
Eventually, Atlantis leaves Earth and resettles on a new planet. The expedition reestablishes contact with their Pegasus allies and learns that the Wraith are being united under a single Wraith Queen called Death.
The expedition eventually launches an attack and is successful in temporarily stopping Death. However, a distress call is received from New Athos and as the Atlantis team arrives to investigate, Meredith Rodney McKay, the Chief Science Officer of the expedition is captured by Darts in a Wraith ambush.
The team regroups in Atlantis and launches a rescue attempt in the hope of saving McKay from Death's clutches, only to discover that McKay has been transformed into a Wraith called "Quicksilver" who believes that he has always served Queen Death.
Eventually McKay is saved and his transformation is reversed. After Teyla kills Queen Death, peace is established between the Tau'ri and the Wraith who cede half of the Pegasus Galaxy to the humans including New Athos and Sateda.
Following the end of the war, McKay becomes obsessed with the idea that Doctor Elizabeth Weir, last known to be trapped in space in Replicator form is out there somewhere as an Ascended being and saved him when he was in trouble.
The team locates an amnesic Weir who is once more human after Ascending with the help of an Ascended Asgard named Ran and was then sent back for interfering to save McKay. However, while Weir eventually regains her memory, the Vanir begin going after her in hopes of getting to Ran and forcing her to descend, believing that as an Asgard that existed before their race began cloning themselves and thus before the degradation, her genetic material could be the key to saving their race.
While working on stopping the Vanir, tensions rise with the Wraith when they demand Atlantis deal with a man known only as "Wolf" who is causing them trouble. The situation with Wolf takes an unexpected turn when Wolf turns out to be long-missing team member Lieutenant Aiden Ford.
Finally a peaceful resolution is reached where Ford will return to Earth and the Wraith will be satisfied.
At Weir's suggestion, the team takes Vanir leader Dis to Earth to communicate with Ran directly through an Ancient shrine and ask for her help rather than forcing it. Ran agrees to help and departs with the Vanir in an attempt to save her race.
Ford is reunited with his family on Earth while Weir is sent back to Atlantis until her humanity is confirmed, but she shows indicators of not desiring to remain there afterwards.
- Stargate Atlantis: Legacy: Homecoming (formerly Stargate Atlantis: Legacy: The Return) (Release Date: September 2010)
- Stargate Atlantis: Legacy: The Lost (formerly Stargate Atlantis: Legacy: The Missing) (Release Date: January 2011)
- Stargate Atlantis: Legacy: Allegiance (Release Date: November 2011)
- Stargate Atlantis: Legacy: The Furies (formerly Stargate Atlantis: Legacy: The Avengers) (Release Date: June 28, 2012)
- Stargate Atlantis: Legacy: Secrets (Release Date: August 2012)
- Stargate Atlantis: Legacy: Inheritors (Release Date: February 2013)
- Stargate Atlantis: Unascended (Release Dates: July 10, 2014 (eBook), July 24, 2014 (paperback))
- Stargate Atlantis: The Third Path (Release Dates: July 16, 2015 (eBook), November 19, 2015 (paperback))