Before his first mission, Ellis and the Apollo were in Earth orbit when seven Ori warships came to attack Earth. He detected their entrance into the Solar system and reported to Major General Henry Landry in Stargate Command that they were holding position for the time being. (Stargate: The Ark of Truth)
On the Apollo's first voyage to the Pegasus galaxy, Ellis commanded a mission to launch a preemptive strike against the Asuran homeworld using the Horizon weapons system. The nature of Ellis's mission led to some friction with Dr. Elizabeth Weir; Ellis bluntly dismissed her objections, stating that not only did he disagree with her, but she had no authority to countermand his orders anyway. When an Asuran counterattack left the city under siege, most of the senior expedition members began to display a degree of hostility toward him, if not outright dismissal. He took issue with Weir's decision to open a dialogue with the Asurans, to which Weir responded by throwing his own words back at him. He was rebuffed just as bluntly by Dr. Rodney McKay when he expressed approval for a plan to submerge the city.
Despite the bumpy start, Ellis held the Atlantis team members in considerable regard, even telling Lt. Colonel John Sheppard that he, not Weir, should be in charge of the city, although Sheppard expressed no interest in such a promotion. He also apologized to Weir for any interference with her command, acknowledging that he was used to being in charge and telling her that, while he knew she didn't like him, and was "not that crazy" about her in turn, he did respect her—which Weir noted distinguished him from others in the military.
Following the mission, Ellis and the Apollo remained in orbit over Atlantis, and was present when it became necessary for the city to depart from the planet Lantea. In preparation, he took all nonessential base personnel aboard the Apollo. (SGA: "First Strike")
When Atlantis dropped out of hyperspace too early, Ellis contacted Colonel Samantha Carter and Dr. Bill Lee on the Midway space station to see if they had heard from Atlantis. The two then joined the Apollo in the search for Atlantis with Ellis expressing doubts about their search plan. After the Apollo finally found Atlantis, Ellis led his ship back to Asuras upon learning of Sheppard's team's mission there. Ellis and the Apollo arrived in time to save the team's lives and Ellis personally contacted Sheppard to inform him of their arrival and urge Sheppard to land his Puddle Jumper on board the Apollo. After Carter couldn't find any sign of Weir's locator beacon the planet, Ellis took the Apollo to hyperspace after Sheppard's Puddle Jumper landed aboard. (SGA: "Adrift", "Lifeline")
During their subsequent attempts to plant satellite beacons to better monitor the Wraith-Asuran war, Apollo recovered a ship containing Angelus, who claimed to be the Ancient survivor of a dead planet. However, it was later revealed that he was actually the creation of the Hybrid, an Asuran experiment to create a Human/Nanite amalgamation that had gone rogue. Ellis was able to drive the Hybrid fragments that had remained on Apollo out of the airlock after the ship was forced to hide in a Gas giant. After Atlantis discovered the Hybrid's planet of origin, Ellis took Apollo to the planet, where he had a brief confrontation with an Asuran ship commanded by Oberoth. Despite the hostility between the two sides, Ellis noted that, since they both wanted the Hybrid destroyed, it made more sense to go along with their currently mutually compatible goals and then return home without engaging in conflict themselves, Oberoth noting the logic of Ellis's decision. (SGA: "Angelus")
Several months later, the Apollo, together with the Daedalus, returned to Atlantis, this time upgraded with the new Asgard plasma beam weapons which they used to destroy several Asuran ships. He was quite rude to Dr. Rodney McKay during the planning, cutting him off several times as he attempted to explain the plan in his usual style.
Enraged at Ellis's treatment of McKay, Colonel Samantha Carter stepped in and stopped Ellis from leaving seconds after McKay had left the room, telling him in no uncertain terms that if he spoke to anyone like that under her command again, regardless of whether they were a civilian or military personnel, he would become persona non grata on Atlantis.
Later the Apollo took part in the Battle of Asuras, which resulted in the destruction of the planet and most of the Asurans, thanks to Dr. McKay's plan. Ellis expressed pleasant surprise, almost shock, at it working right in front of him although he was clearly happy at the result. McKay said he wanted to have seen his face when it did work. (SGA: "Be All My Sins Remember'd")
In 2009, he was ordered to engage a Super-hive before it was to reach Earth. Despite assistance from the Sun Tzu, both ships were crippled. He sent a distress signal to Atlantis, informing them that without hyperdrives, it would take at least one month until they reached the nearest Stargate. (SGA: "Enemy at the Gate")
A gruff hard-nosed military man at heart, Ellis often prefers the military way of doing things and has little or no patience for any civilians associated with Stargate Command or even the Atlantis Expedition which is demonstrated in his conversations and meetings with both Dr. Elizabeth Weir and Dr. Rodney McKay, both of whom he treats with great dislike or disrespect. He also has no patience for those who waste his time, often cutting people off who he feels take too long to explain things, preferring simple "yes or no" answers, and only wanting a protracted explanation when he feels it is absolutely necessary.