In the event the facility was ever in danger of being taken over, a single person was to remain behind and activate the Operation, detonating the explosives planted under the facility in order to destroy the base and prevent its secrets from being captured by the Covenant.
The operation also called for the destruction of every AI present using the fail-safe in its Riemann Matrix before the base was destroyed, thus ensuring that the Covenant did not capture that technology before the base was destroyed. Unfortunately, it seems that the Covenant also have some sort of Artificial (or Associated) Intelligence.
In 2552, during the Battle of Reach, Dr. Catherine Halsey was left behind along with several AIs, including Kalmiya and Araquiel. When the Spartans arrived at the facility, Halsey activated the operation and destroyed the facility and both AIs. She, Frederic-104, William-043, Vinh-030, Isaac-039, and Kelly-087 were able to hide in the caves beneath the base. They were able to stop the Covenant from accessing the secrets of the base, but they were trapped under the base for several days.