Command Neural Interface implants are implanted in the brain of every UNSC ship commander. In addition to the duties of a standard Neural Interface, they also have several purposes specific to a ship commander.
Once installed, they cannot be removed without killing the host and are therefore permanent. Their main use is the storage of data codes, NAV data, and also for receiving telemetry from outside sources. AIs can access the lace with the owner's consent and retrieve data for use. The owner of the lace can also receive data about the ship they command, sent directly to their retinas courtesy of the shipboard AI. The CNI Transponder of the commanding officer is the only thing with clearance for initiating a vessel's auto destruct. This way, the only way a ship may be destroyed is if its commander authorizes the destruction, or if the commander is dead, their interface may be removed. Although permanent, they can be upgraded for specialized functions, such when as the Master Chief's CNI was upgraded in The Fall of Reach.
In the level Keyes, the Master Chief recovers the Command Neural Interface from the body of Captain Keyes, whose Flood-infested form had to be killed in order to retrieve it.
In Halo 3, The hidden skulls have a Command Neural Interface at the back, it can be clearly seen in Theatre Mode.