On the level The Covenant, in the tower where Sergeant Johnson was supposed to deactivate the tower, there is a Secret Room right underneath the tower controls. To get into the room, you will need to get out of the level with a Hornet and fly into the tower from the back. This room is believed to be what controls the elevator that the John-117 uses to get up to the tower control room. The real purposes of this room is still unknown.