Faced with the threat of the Wraith, Woolsey tells Dr. Weir that the IOA is considering bringing the Atlantis ZPM to Earth to power the Ancient defense platform in Antarctica. He is also part of an IOA panel that recalled Dr. Weir to Earth to explain her failed alliance with the Wraith. He genuinely respects Weir and attempts to defend her actions, but must defer to his IOA colleagues. The IOA dispatched him to Atlantis to evaluate Weir's ability to command. While evaluating Weir's abilities, he made a rather poor impression on the expedition members (Lt. Col Sheppard expressed a strong desire to knock Woolsey on the head). However, he ultimately sides with Weir by sending the IOA a report modified to favor Weir and keep her in command of Atlantis. When live Ancients were found and reclaimed control of Atlantis, Woolsey and General O'Neill were sent to negotiate with them. Woolsey and O'Neill were allowed to stay as liaisons with the Ancients, and both were trapped when the Asurans invaded and took control of the city. They were eventually rescued by members of the former Atlantis expedition, although Woolsey expressed frustration that he had been duped as a part of the rescue plan.