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An isolation door was a special reinforced door designed to separate a hazardous area from the rest of a starship or space station. Isolation doors were often employed in main engineering, specifically to seal off the warp core and dangerous antimatter reactants in the event of a warp core breach or loss of antimatter containment.
Main engineering aboard the Galaxy-class USS Enterprise-D was equipped with at least two isolation doors. The outer isolation door served to separate the warp core and engineer's office from the rest of engineering, the inner door only separated the warp core from the rest of engineering, in an emergency, the engineer's office would still be accessible.
In mid-2369, Captain Jean-Luc Picard sabotaged the warp core in order to escape a group of terrorists who used the evacuation of the Enterprise for routine maintenance as an opportunity to steal highly valuable, and highly dangerous, trilithium resin from the core. Picard triggered a coolant leak which caused the outer door to close automatically. (TNG: "Starship Mine")
Isolation doors were also used in the nacelle tube control rooms aboard Galaxy-class starships. The isolation doors could be opened with the protection of a one-way force field. The doors, however, could only remain open for ninety seconds in order prevent force field degradation and the release of drive plasma. (TNG: "Eye of the Beholder")
In an alternate timeline created when the USS Enterprise-C disappeared from the Battle of Narendra III, the isolation door was used in a vain attempt to contain a coolant leak during a Klingon assault. (TNG: "Yesterday's Enterprise")
Some starships, like the Intrepid-class lacked isolation doors, as their engineering sections were extremely open and were separate from the rest of the ship with no open corridors leading to the area. (VOY: "Day of Honor", "Waking Moments")
In Star Trek: Elite Force II, the isolation door can be seen closing as the player character approaches the engineering section during the Idryll attack.