Before the Wraith Hive ships arrived in the Lantean system he flew a Puddle Jumper with Dr. Rodney McKay and Dr. Peter Grodin to the only remaining Lagrangian Point satellite which McKay hoped to get up and running before the Hive ships arrived. After Rodney went on board the satellite in a space suit, he used a Naquadah generator to provide power to the satellite. And when the satellite had power, he and Grodin joined McKay board and the three of them began working to get the weapon online. When Grodin found the system that enabled anti-gravity, he told Rodney that he should grasp something before Grodin enabled the system. But gravity came on too quickly and McKay fell straight to the floor, believing he had suffered permanent back damage.
Miller saw Rodney fell and then helped him up. But they all quickly discovered that the energy went directly to the weapon but did not activate it. And they discovered that in order to get the weapon that one of them had to go outside of the satellite and activate the panel. They drew straws, and Rodney was the one who went out and turned on the panel.
When the Hive ships came, Miller and Rodney returned to the Jumper, leaving Grodin behind on the satellite to shoot the gun. They eventually returned to Atlantis after witnessing the Hive ships attack and destroy the satellite, killing Peter Grodin in the process. (SGA: "The Siege, Part 1")
A year later, Miller flew one Puddle Jumper in orbit around the M6R-867 and scanned the planet to see how many Genii that were on the planet. He then returned to Atlantis and reported his findings. (SGA: "Coup D'etat")
When Lt. Colonel John Sheppard's team were captured on a mission to a Wraith lab, he piloted the Puddle Jumper with Colonel Samantha Carter, Ronon Dex and Dr. Radek Zelenka on a rescue mission. (SGA: "Reunion")
When Major Evan Lorne led a team to repair the Atlantis underwater scanners in order to get the city's ice defenses working again, Miller pilots a Puddle Jumper that is used to monitor the repairs and broadcast it back to Doctor Radek Zelenka. (SGA: "The Lost")
- Miller appears to be the only commissioned officer not on the first Atlantis team of the original Atlantis expedition. All other mentioned military personnel are enlisted. It's also possible he is the second highest ranking officer of the Original Expedition after Colonel Sumners death, depending on if he or Ford has seniority.