I'm looking for a fic which is set earthside. The city of Atlantis is anchored in San Francisco Bay. John is held prisoner somewhere nearby and tortured because the bad guys (some sort of government agency) want to make him their human weapon. Rodney finds out and sets about freeing John, mostly all by himself. They then hide on a boat which Rodney bought from an ex-soldier, who ends up helping them. I think they leave earth permanently in the end - not sure if with or without Atlantis.
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