Vice-President Kinsey wanted to use Weir as a civilian "puppet" to achieve his goals to gain control of the Stargate program.

Dr. Weir remained the Chief of Stargate Command during the fallout from the battle and impressed her senior staff when she successfully bluffed Earth's position during tense negotiations with a delegation of System Lords.

Not long afterwards, Dr. Weir accepted reassignment to the Antarctic Research Outpost and its international staff, which she felt was better suited to her skill set.

[1] Some 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.

[5] 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.

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.

She took part in a mission to save Atlantis by stealing a Zero Point Module (ZPM) from the Asurans and sacrificed herself to allow the team to escape.

[8][failed verification] Showrunner Joseph Mallozzi mentioned the possibility that a Replicator lied to or misinformed the Atlantis team when she said that Weir was killed.

This clone of Weir is believed to have been killed by a contingent of Asurans when she sacrificed herself to allow the original Sheppard, Ronon, Teyla and McKay to escape.

Once Elizabeth convinced Col. Sheppard and Mr. Woolsey that they would not be a threat to Atlantis, they proceeded to work on creating organic bodies into which they could download themselves.

After Weir saves McKay's life, she is forcibly de-ascended as Doctor Daniel Jackson once was and is found by the team, human once more.

Weir aids the team in dealing with the Vanir - a rogue faction of Asgard - and returns to Atlantis until she is confirmed to be human once more.