After Samantha Carter takes control of Atlantis, Woolsey once again returns in order to assess her ability to command the expedition. Once again he finds himself in the middle of a dangerous situation, including coming face to face with a Wraith for the first time. Eventually he leaves and apparently presents a favourable report of Carter's methods. Although he had claimed to want to produce a report which was as thorough as possible, he indicated to Carter that certain facts would be left out to make the report more favourable to her. In an alternate timeline Woolsey became the leader of Atlantis, after Carter was killed in a kamikaze run against three Hive ships. In this timeline, he ordered every resource in Atlantis to focus on the protection of the city and recalled everyone trying to help other humans in the galaxy who had fallen victim to Michael's plans for galactic domination.