The Jumper bay, which is located on top of the central tower of Atlantis, houses the small ships. The room is a large two-floor room which can store the 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 the Jumpers to leave it: the first is a large panel in the middle of the floor which leads directly to the large platform of the gate room, so that the Jumper can fly immediately through the Stargate. The second possibility is another panel that is located in a small shaft in the ceiling and thus allows the Jumper to leave the city to fly to other locations on the planet or star system. This panel was however discovered later.
History
While the Asurans controlled Atlantis, Sheppard flew a Puddle jumper into the control room and dropped a payload. The explosive detonated and destroyed the control room and a good part of the tower. It presumably destroyed the jumper bay as well. later, the
Atlantis' underwater bay
Jumper bay was seen intact and its design was different from the first one: It was a much larger room and was not in a perfect circle, meaning that when the Asurans rebuilt the Jumper bay, they may have changed the design.
Atlantis also has an underwater jumper bay on its underside specifically designed for underwater entry and egress. The control station is dedicated to pressurization and pumping system for the underwater bay. The bay was recently used to reclaim the city from Micheal. Rodney McKay repaired one of the water-damaged jumpers and used it to dial the Stargate, destroying Micheal's jumper that had been powering the control tower. (SGA: "The Prodigal")
See Also
The layout of a Jumper Bay