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“[B]eing compelled to stand alone, after having undergone the very extremity of danger,...in a single day and night of misfortune...the island of Atlantis in like manner disappeared in the depths of the sea.” -- Plato
Atlantis, the once fabled city that was thought to be lost to the depths of the ocean, had been found. The city had remained dormant in the bottom of the sea for 10,000 years until an Earth-based expedition set out through the Stargate six years ago and woke the sleeping city from her slumber, raising her from the depths. While cutoff from Earth, the expedition was forced to start anew. Many friendships were formed and even more enemies were made with the inhabitants of the galaxy. Great successes as well as disconcerting losses followed the team as they explored their new home; however, a paramount issue eventually arose and threatened to destroy all they had once known. To defeat a seemingly hellbent enemy, Atlantis - not only a city but an alien spaceship - set out from its destination in the Pegasus Galaxy and towards the aspect of concern - Earth.
The imminent attack on Earth was successfully thwarted, but not without its consequences. The trip weakened Atlantis' power supply to the point where it could no longer return to the Pegasus Galaxy, the place that the city's occupants had grown to know as their home. The city now rests in the San Franscisco Bay, hidden to the rest of the world by a cloak, waiting to some day return to its previous home. At the same time, government and military programs are deciding on the future of both it and its occupants, whose ties are being strained by the vast differences of two distant galaxies...