Dr. Weir was placed in command of the expedition that was sent through the Stargate to explore Atlantis. As a diplomat, Weir sought treaties with the human populated worlds in Pegasus, one of them being the Athosians. There was often tension between her and the leader of the Athosians, and the latter eventually left the city to live on the mainland. At the end of Season 3, she was left in a coma when a beam that the Asurans had created targeted the Control Room of Atlantis, hoping to destroy Atlantis for good. She eventually survived with several nanites that had remained in her system successfully repairing the damage and injuries she had received. She then joined Sheppard's team during a mission to Asuras where they were hoping to get a ZPM to help Atlantis recover once again. In the end, Weir sacrificed herself so that the team could get to safety despite Sheppard's refusal to leave her behind. Her final appearance was in Ghost in the Machine where she returned to the team in a new body but possessing the original Weir's consciousness, personality and memories.