The room is a large two-floor room which can store the Puddle Jumpers on the floor or on platforms on the upper area. The upper area also contains a gangway which runs on the walls and provides access to the platforms. The room provides two possibilities for Puddle Jumpers to leave it: the first is a large panel in the middle of the floor which leads directly to the large platform of Stargate Operations, allowing a Puddle Jumper to fly directly through the Stargate. The second possibility is another panel that is located in a small shaft in the ceiling, which allows Puddle Jumpers to leave the city to fly to other locations on the planet or even star system. (SGA: "Rising", "Suspicion", "The Defiant One")
The Jumper bay is also capable of holding F-302 fighter-interceptors.
Atlantis also has an underwater Jumper bay on the North Pier underside specifically designed for underwater entry and egress. There is a small control station dedicated to the pressurization and pumping system for the underwater bay. This bay, however, is only known to contain at least two Puddle Jumpers and is very seldom used. (SGA: "The Return, Part 2", "The Prodigal")
While the Asurans controlled Atlantis, Lt. Colonel John Sheppard flew a Puddle Jumper into the control room and dropped a payload of explosives; the resulting detonation destroyed both the control room Stargate Operations and a good portion of the central tower, including the Jumper bay, which most likely collapsed. Later, the Asurans rebuilt the Jumper bay, but its design was different from the original: it was a much larger room and was not in a perfect circle, meaning that Asurans may have changed the layout as well. Later, a small team, lead by Sheppard, was able to infiltrate the city through the underwater bay, after it was drained of water by Major General Jack O'Neill. (SGA: "The Return, Part 2")
Atlantis' underwater bay was also used in 2008 to help reclaim the city from Michael Kenmore. Dr. Rodney McKay repaired one of the water-damaged Puddle Jumpers and used it to dial the Stargate, destroying Micheal's Puddle Jumper, via the Stargate's unstable vortex, that had been powering the control tower. (SGA: "The Prodigal")
- In one of the alternate realities that the alternate Daedalus jumped into, Atlantis launched a wave of F-302 fighter-interceptors to combat the Alien fighters attacking the alternate Daedalus, which were likely stored in Atlantis' Jumper bay. (SGA: "The Daedalus Variations")
- In an alternate timeline where Atlantis didn't have a Failsafe mechanism and the city didn't rise to the surface after the shield collapsed, the Atlantis expedition evacuated to the Jumper bay and boarded the ships. However, it was eventually flooded along with the rest of the city. (SGA: "Before I Sleep")