I'm trying to figure out now how to write the story where Atlantis goes back to Pegasus
I've had a couple ideas about that which I'll share because I'm not using them.
Atlantis is infiltrated and hijacked off the planet along with a skeleton crew under threat or if the IOA, etc, remain intent on keeping the whole stargate and aliens thing classified, then they have to fly Atlantis away, because keeping it cloaked 24/7 will drain the ZPMs in a couple of weeks. They send Atlantis back to Pegasus because there are too many enemies eager to take the city for it to be safe anywhere in the Milky Way.
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I've had a couple ideas about that which I'll share because I'm not using them.
Atlantis is infiltrated and hijacked off the planet along with a skeleton crew under threat or if the IOA, etc, remain intent on keeping the whole stargate and aliens thing classified, then they have to fly Atlantis away, because keeping it cloaked 24/7 will drain the ZPMs in a couple of weeks. They send Atlantis back to Pegasus because there are too many enemies eager to take the city for it to be safe anywhere in the Milky Way.