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Jonathan J. O'Neill is a Lt. General, in the United States Air Force, who served seven years in the Stargate Program as a Colonel and also as the leader of the SGC's main team, SG-1.
After being released from stasis a few months after the Battle of Antarctica, O'Neill was promoted to Brigadier General and became the new Commanding officer of the SGC, replacing General George S. Hammond. Jack led the SGC for a year before being replaced by General Hank Landry with O'Neill being reassigned to The Pentagon to become the head of Homeworld Security.
It was now, finally, coming up on time for him to retire--which would move Hank Landry up to Homeland and, had things gone as expected, Colonel Samantha Carter would be promoted to Brigadier and take over the command chair at the SGC.
But in a completely unexpected move, Carter had chosen a different path. She had stolen Atlantis and returned to the Pegasus Galaxy. Her motives were pure as the damn driven snow but it was the fact that she had never - not once! even so much as hinted at what she was doing to him.
Part of Jack O'Neill was honest enough to admit that if she had, he would have had to choose to either stop her or go with her. Neither of which would have been his choice. What he'd wanted was never going to happen as it would have been a completely different future with Samantha Carter as part of that future.
Now, he had to arrest her. Not at all how he had seen the future.
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