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The isolation protocol, also known as confinement mode, was the name of a computer protocol on Starfleet ships. Triggered by the computer's detection of a hull breach, emergency bulkheads are closed to isolate sections of a starship. (TNG: "Disaster")

The USS Enterprise-D encountered a quantum filament that triggered a hull breach and consequently the computer executed this protocol, isolating senior staff in different areas of the ship. Prior to this event, Counselor Deanna Troi was unfamiliar with the protocol. Chief Miles O'Brien explained it to her, as holding the rank of lieutenant commander, she was the senior officer at the time. (TNG: "Disaster")

A similar protocol was used in TOS: "Day of the Dove", however, the bulkheads were closed not by the computer sensing a hull breach, but rather the Beta XII-A entity that closed the bulkheads to even the Starfleet and Klingon forces aboard the Enterprise.
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