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John and his Team work for Elizabeth Weir, as covert agents, at Atlantis Expedition, a government agency. While chasing a lead about recent activities of Minister Cowen, they are tricked and gassed. Later they find Rodney has been kidnapped by the evil Minister.
They are even more suprised when a man from the past, who has his own agenda, offers information on their kidnapped scientist, but Only if Sheppard agrees to the man's terms.
There is also the matter of the Spy, which again their dubious ally claims to know who it is. Can they trust him.