time after Dr. Weir was sent to lead the research envoy studying the Ancient defense facility that had been discovered in Antarctica, Daniel Jackson realized that the lost city of Atlantis was located in the Pegasus Galaxy. Dr. Weir was placed in command of the multinational 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 of the planet where Atlantis was hidden. Weir approved several projects throughout Atlantis in season two including the Wraith retro-virus that she later gave as part of a treaty to a sect of Wraith looking to replace the human food source with Wraith infected by the virus. The retro-virus suppressed the Wraith genetic material in the DNA of a Wraith, leaving only the human DNA. Weir became infected with the consciousness of an alien soldier named Phoebus that was at war with another consciousness called Thalan who also took over John Sheppard. Both rampaged through the city, triggering a hostage situation which was caused by the aliens' desire to defeat one another for good. After nearly 24 hours, the rogue consciousnesses were subsequently expelled, resulting in both Sheppard and Weir returning to normal once again. In season 3, Weir's leadership abilities were questioned by the International Oversight Advisory (IOA) Committee after two Wraith hive ships attempted to attack Earth. Although she managed to stop both hive ships, the IOA was divided over whether she should be allowed to remain leader of Atlantis and it was only with some help from Richard Woolsey that she was able to keep her position. She also unsuccessfully tried to negotiate an alliance with the Asurans and was infected with Asuran nanites. They later tried to assimilate her body and she very nearly didn't survive. In the final episode of season 3 ("First Strike") Weir was critically injured by the Asuran Satellite Weapon, leaving the city without a leader and adrift in space. The season 4 premiere episode "Adrift" revealed that Weir had suffered massive injuries. She was later healed by the Asurans Replicator nanites that were left dormant in her body from when she was infected by Niam. As a result of this treatment, she