||Dr Daniel Jackson, discovers the true location of the Ancients lost city of Atlantis, in the pegasus galaxy. The SGC decides to send a new Stargate Team to the lost city, once there they encounter another planet of primitive humans, and a new fearsome enemy the Wraith.
||Sheppard tries to convince Dr. Weir to mount a rescue mission to free the natives, and team members captured by the Wraith. Mean while Colonel Sumner faces the Wraith themselves.
||Hide and Seek
||An alien intruder has found it`s way into the city, threatening the security of the base. Dr McKay`s experiments with alien technology lands him in trouble.
||The Atlantis Team`s "Puddle Jumper" shuttle becomes trapped in the eventhorizon of stargate located in orbit of an alien planet.
||Having encountered Wraith on nearly every mission, the Earth team begin to suspect, a traitor amongst the Athosians, and Teyla finds herself caught in the middle.
||The team crash lands on a planet inhabited by children all under the age of 25. The team discovers that the children pratice ritual suicide in fear of the Wraith.
||Poisoning The Well
||The team finds a world whose people are on the brink of a discovery that may make them immune to the Wraith feeding.
||Efforts to open trade relations with a species called the Genii turn sour when the team discovers their new "allies" have ulterior motives.
||McKay`s efforts to harness the energy of an alien planet`s atmosphere allows for a return trip to Earth -- but the team may not be able to return to Atlantis.
||When a massive storm threatens the city, Atlantis is evacuated -- only to be taken over by the team`s newest enemy.