Colonel Samantha Carter (Amanda Tapping) left her command role to return to Earth for the Stargate SG-1 storyline "Continuum" and to pursue other projects.
Richard Woolsey (Robert Picardo) took command of Atlantis, transitioning from a bureaucratic adversary to a dependable ally. Stargate Atlantis - Season 5
Dr. Carson Beckett returned as a regular recurring character after his clone was rescued and stabilized. Colonel Samantha Carter (Amanda Tapping) left her command