Stargate Atlantis returns with another brand new story continuing the adventure of the classic sci-fi television show in comics! Picking up right where the TV series left off, this new arc continues the breathtaking events of STARGATE ATLANTIS: BACK TO PEGASUS! The team is faced with danger at virtually every turn as Janus forces the immediate evacuation of Atlantis from Earth, which throws the city into chaos and sets in motion a deadly, new chain of events. Main cover by Matt Wieringo, Subscription variant cover by Ken Haeser & Buz, and SGA Photo and Retailer Incentive Photo Flashback covers.
The events depicted in this adventure take place after Stargate Atlantis: Back to Pegasus series, which took place after season five of Stargate Atlantis.
Earth, Milkyway Galaxy: Atlantis takes off from Earth and enters hyperspace. Dr. McKay informs Col. Carter and Mr. Woolsey that they can dump the extra energy from the overload into the city's shields or the wormhole drive. If that doesn't work, the results would be and explosion or decompression. After using the After Wormhole Drive, the overload is prevented.
Atlantis comes to a stop at the edge of the Pegasus Galaxy. There are still major repairs that need to be done and because of Janus, the main computer can't be trusted for the time being, so it is taken offline.
They set course for the plant they left when the traveled to Earth to fight the Super-hive. Because the computer is offline, there needs to be someone with the ancient technology activation gene operating the control chair around the clock. The city arrives at the planet and Col. Sheppard lands the city on the ocean.
Pegasus Galaxy: After Atlantis lands, it is decided to restore the computer using a backup file to avoid anything that Janus may have done to the software. Since restoring the whole backup would take longer then they would want, the operating system portion of the backup is restored first.
After learning that the Earth control crystal was destroyed at the Alpha Site, Sheppard orders McKay to get his stuff. meanwhile Janus is being interviewed.