Origin is a direct continuation from the two-part season opener, Avalon, wherein we were first introduced to Ben Browder as SG-1's new leader, Lieutenant Colonel Cameron Mitchell. Originally intended to be a stand-alone episode, executive producer Robert C. Cooper says in the Season 9 companion book that it just wasn't possible to conclude the opening story at the end of Avalon:

In 2005, Stargate Command was forever changed. The former leader of Blue Squadron and hero of the Battle of Antarctica against the forces of Anubis - the man who protected SG-1, sacrificing himself and breaking his back and legs in the process, who almost became a quadriplegic, yet made a miraculous recovery - Lieutenant Colonel Cameron Mitchell, was given command of the elite team SG-1