After discovering the mysteries behind the eighth chevron and with a partially powered ZPM Stargate Command decide to send an small expedition to the Pegasus galaxy where they hope to meet the Ancients. However upon entering the Lost city of Atlantis, what the Expedition discover is a threat far worse than even the Goa'uld... and they're now awake.
With the Wraith's siege of Atlantis continuing, Stargate Command sends the Daedalus along with a fully powered ZPM to save the city. However even with the battle won, with the Wraith knowing the location of Atlantis, can they win the war? The
Having defeated the Wraith Hive Ship that was heading to Earth, the Atlantis Expedition have a hard choice as to what to do to the Wraith-Human Hybrid's. Exploring the Pegasus galaxy the expedition soon discover what they believe to be a new ally against the Wraith - the Lanteans that they had come to the Pegasus galaxy to meet, however they don't appear to be who they seem, and soon the expedition are forced to launch a first strike.