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Ventilation systems were used throughout buildings, starships, starbases and other facilities to direct and control the flow of breatheable atmosphere. (TOS: "The Trouble with Tribbles"; VOY: "Year of Hell, Part II", "Message in a Bottle")
In 2268, on stardate 3619.2, the Dikironium cloud creature entered the USS Enterprise's ventilation system and subsequently killed one crewman and severely injured another. Captain James T. Kirk, Commander Spock and Doctor Leonard McCoy then met and decided to drive the creature out of the ventilation system by flooding the system with radioactive waste. (TOS: "Obsession")
Later that year, on stardate 4523.3, Tribbles infested Deep Space Station K-7 by moving through the station's ventilation ducts allowing them access to the station's grain storage area. (TOS: "The Trouble with Tribbles")
In 2269, on stardate 4978.5, the crew of the Enterprise became intoxicated by the effects of Harry Mudd's love potion, which was disseminated throughout the ship using the ventilation system. (TAS: "Mudd's Passion")
In 2374, on stardate 51425.4 (Day 133 of the Year of Hell), the ventilation system on board the USS Voyager began to fail as a result of constant attacks from the Krenim Imperium which allowed gas from a Class 9 nebula to flood one of the last habitable decks on the ship. (VOY: "Year of Hell, Part II")
Later that year, on stardate 51462, The Doctor and the EMH Mark II of the USS Prometheus dispersed neurozine gas throughout the Prometheus using the ventilation system, incapacitating the Romulan hijackers. (VOY: "Message in a Bottle")