 A spaceship appears out of nowhere over Atlantis . John Sheppard ( Joe Flanigan ) and his team discover that the ship is the Daedalus , which is strange as Stargate Command confirms that the Daedalus is actually two days away from Earth . Sheppard 's team boards the new Daedalus and find it apparently abandoned with signs of battle damage . Teyla ( Rachel Luttrell ) views a log entry from the Daedalus commander , Colonel Sobel , who the team has never heard of before . Suddenly , there is a power spike and the Daedalus disappears from above Atlantis , while from the perspective of Sheppard 's team , Atlantis disappears . McKay finds that they have been propelled into a parallel universe by what he terms an " alternate reality drive " , and thus the Daedalus is actually from an alternate reality . 
