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.

A significant romantic arc developed between Dr. Rodney McKay and Dr. Jennifer Keller, though it received mixed reactions from the fanbase. Major Story Arcs and Notable Episodes Stargate Atlantis, Season 5: mariness - LiveJournal

Dr. Carson Beckett returned as a regular recurring character after his clone was rescued and stabilized.