Joker was pilot of the Normandy SR-1 when it was commanded by Captain David Anderson and, later, Commander Shepard. The Normandy discovered the geth attack on Eden Prime, lead by the renegade SPECTRE Saren and the Reaper Sovereign. Joker piloted the ship throughout Shepard's mission to track down and defeat Saren, eventually firing the torpedoes that killed Sovereign at the Battle of the Citadel.
Following the destruction of Sovereign, the Citadel Council allowed Shepard to continue his search for more evidence of the Reaper threat. During this mission, the Normandy SR-1 was ambushed and destroyed by the Collectors. With Shepard killed in the attack, the Council and the Systems Alliance dismissed the threat, abandoned the mission, and dispersed the surviving crew members.
Two years later, Cerberus managed to return Shepard to life and provide him with a new ship, the Normandy SR-2, to investigate attacks on human colonies in the remote Terminus Systems. The Illusive Man used his information network to identify and recruit several members of the Normandy SR-1 crew to serve on the SR-2, despite them having to leave Systems Alliance service to do so. Joker was one of the recruits, returning to his role of pilot. Following the Aratoht mission, which resulted in the deaths of over 300,000 batarian colonists, Shepard and Joker were relieved of duty pending a full investigation.
Joker assisted Systems Alliance engineers in refitting the Normandy SR-2 to Alliance specifications while Shepard was in custody. When the Reapers attacked Earth, Joker was on board, and he resumed piloting duties when Admiral Anderson reinstated Shepard and ordered them off planet to seek reinforcements to fight the Reapers.
Joker has Vrollik's Syndrome, a chronic condition that causes his bones to be extremely brittle.