Kate Holmes had been part of several SG missions with Dr. Daniel Jackson as he tracked down and catalogued Ancient lore and technology. A promotion, however, offered a chance to join the crew of the Daedulus and go to the Pegasus Galaxy to see the fabled, and now found, City of Atlantis.
That was just too good a chance to pass up so Cmdr. Kate Holmes of the U.S. Navy found herself on a ship with a crew from both Air Force and Navy who got along surprisingly well. At heart, she realized they were all too much interested in the exploring that they would get to do to worry about such things. Which suited her just fine.
Until the day that word came about Colonel Samantha Carter's hijacking the City and taking it back to the Pegasus Galaxy. Once there, things got even weirder as her commanding officer, Colonel Stephen Caldwell told the twelve members of the quickly assembled skeleton crew of the Daedulus that he (and the ship!) were going to stay with the City and they each had a life altering choice to make:
Stay and become part of the breakaway group thus pretty much destroying their lives back home or go back in a pre-programmed, one-way shuttle whose controls would be locked out and preset to implode once they reached home thus making it impossible for the SGC to use it to track back to Atlantis.
Hell of a choice...
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Alas, the Folly of Man