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. (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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