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According to Cooper, Stargate Universe "maintains the spirit of Stargate, but opens up a whole new 'universe'."[3] It is "a completely separate, third entity"[4] – as opposed to Stargate Atlantis, which was created as a spin-off from the first series Stargate SG-1. Like the first two series in the franchise, Stargate Universe will take place during the present time, not in the distant future.[4] The show will be "set on a ship that was part of an Ancient experiment" to seed the galaxies with Stargates millions of years ago but that was prematurely ended by the Ancients' ascension. After placing Stargates throughout multiple galaxies, a second ship would follow up and explore.[5] When a team of explorers from Earth find an Ancient unmanned ship called the Destiny and are unable to return to Earth, the crew must fend for themselves aboard the ship as it takes them to the far reaches of the universe.[2] The basis of Stargate Universe is that the ninth and final chevron, the purpose of which was previously unknown, would serve to get to the first ship.[5] The show will involve more space-based action than SG-1 or Atlantis.[2]

After unlocking the mystery of the ninth chevron, a team of explorers travel to an unmanned starship named The Destiny, which was launched by The Ancients as an experiment, but was never completed. The crew will travel throughout the universe, and eventually fulfill the Destiny's original mission.