Michael played archaeologist Dr. Daniel Jackson throughout the first five seasons of Stargate SG-1 before leaving the show, citing creative differences concerning the under-use of his character and the direction of the show as a whole. He made several guest appearances throughout the sixth season playing his own character, as well as voicing the Asgard character Thor. Shanks returned for the seventh and subsequent seasons, winning the Leo Award for Best Lead Performance By A Male in a Dramatic Series in 2004 for the seventh season episode "Lifeboat". During the series' tenth and final season, he signed up for 16 of the 20 episodes, taking some time off in March 2006 for the birth of his third child (second with wife and occasional co-star Lexa Doig).
He appeared in both direct-to-DVD Stargate films released in 2008; Stargate: The Ark of Truth and Stargate: Continuum, and won the 2009 Leo Award for Lead Performance by a Male in a Feature Length Drama for Continuum.
In 2004, Shanks made a crossover appearance (as Daniel Jackson) in the Stargate Atlantis pilot, "Rising". He also appeared in the tenth and eleventh episodes of Atlantis' fifth and final season, and made a cameo appearance in the pilot of the third Stargate series Stargate Universe