Colonel in the United States Air Force, commander of the Deep Space Carrier U.S.S. Apollo. Ellis was first dispatched to the Pegasus Galaxy with intelligence regarding the Asurans, Pegasus Replicators who were busily constructing a series of warships to attack Earth. A preemptive assault was planned and conducted by the Apollo, which launched a series of Mark IX tactical nukes into Asuras's atmosphere.
Ellis had a tumultuous relationship with Dr. Elizabeth Weir during her final days as leader of Atlantis, but he did make her aware that though he didn't necessarily care for her, others in the military (such as General Jack O'Neill) were very fond of her. Ellis later had to contend with Colonel Samantha Carter, who replaced Weir as leader of Atlantis.
A no-nonsense commander and military strategist, Colonel Ellis continues to play a vital role in the defense of Earth and its interests as commander of the Apollo.
First Strike - Ellis commands the Apollo during a preemptive assault on the Pegasus Replicator homeworld.
Adrift - Ellis begins a search for Atlantis, which is lost in space.
Lifeline - Ellis gives Colonel Samantha Carter and Dr. Bill Lee a lift from Midway Space Station.
Be All My Sins Remember'd - Ellis commands Apollo into battle over Asuras once again, this time in cooperation with the Daedalus, the Wraith and the Travelers.
Enemy At the Gate - Ellis and the Apollo attempt to stop an advanced Wraith warship headed for Earth, but both the ship and the Sun Tzu are left crippled by the battle.