- Base Key - Given to Strifeguy by Rowan. It allows access to the Front Base
- Gov's Key - Received from Macil after first meeting him, it allows access to Governor Mourel's mansion. It is also possible to acquire this key by trusting Harris and completing his quest to steal the offering chalice, though this causes the game to reach a dead end.
- Pass Card - Governor Mourel gives this to Strifeguy upon accepting his "bloody" task. Grants entry to the Power Station. If not obtained this way, the key is again given to the player by Macil when asked to destroy the power crystal.
- Prison Pass - Governor Mourel gives this to Strifeguy upon return after either of his missions is completed. Opens the prison gate.
- ID Badge - Optional key from the Prison Guard, drops upon his death. Gives access to Warden Montag. Speaking to the guard will also open the locked door automatically.
- Prison Key - Key dropped by Warden Montag upon death, allows entry into the majority of the prison. Any key slot that is yellow in the prison can be activated by this key.
- Severed Hand - Taken from Judge Wolenick, it allows Strifeguy to use hand scanners and free the prisoners.
- Power1 Key - Given by Worner during Macil's Power Station Mission, it allows access to the reactor core sector of the Power Station. This key can also be obtained by killing the red acolyte guarding the core entryway, but only if the key is manipulated into landing on the window sill. This constitutes a sequence break.
- Power2 Key - A technician gives this to Strifeguy, allowing access to the western reactor core sector of the Power Station. It can also open a door blocking access to the technician holding the Gold Key, though he can also be approached from the other direction with the Power1 Key.
- Gold Key - Dropped by a technician who talks about new weapons. Allows access to the weapons cache in the warehouse sector of the Power Station mentioned by Worner.
- Power3 Key - Given by Sammis, used to gain entry to the reactor core. Also opens the sewer overflow gate in Tarnhill.
- ID Card - Dropped by two red acolytes in the sewers. Used to open a storage sector in the sewers which contains a grenade launcher.
- Silver Key - Obtained from the False Programmer in the Audience Chamber, it opens caches in the abandoned Front Base and in the Audience Chamber, and grants access to the Programmer's Keep.
- Oracle Key - Dropped by two red acolytes in the Borderlands; allows entry to the Temple Of The Oracle.
- Military ID - Given by the Keymaster after the Oracle grants his permission. Opens the gates to the Bishop's sector of the Borderlands.
- Order Key - Dropped by a gray Acolyte in the Bishop's sector of Borderlands, and by a red acolyte in the Bailey. Allows access beyond the initial portion of the Bailey.
- Mauler Key - Dropped by a gold acolyte in The Fortress: Stores. Allows access to the room containing maulers.
- Core Key - Located on a pedestal in the northwest area of Fortress: Administration; allows access to the central computer.
- Brass Key - Given by Macil after killing the Oracle, it grants access to the Order Commons.
- Catacomb Key - Given by Richter; ostensibly grants entry to the Catacombs; however, the door to the catacombs is also automatically opened when talking to Richter.
- Mine Key - Found under a Spectre in Catacombs: Ruined Temple. It opens the door to the mines.
- Factory Key - Found under a Spectre in the Ruined Temple, it opens the main gate to Factory: Receiving.
- Blue Crystal Key - Found in Factory: Conversion Chapel; it is required for access to the converter.
- Red Crystal Key - Found in the Conversion Chapel, it is required for access to the converter.
- Chapel Key - Found in the Conversion Chapel. It is required to obtain one of the two crystal keys.
The locked messages for the ID Badge and ID Card are switched: doors opened by the ID Badge give the message "You need an id card"; while doors opened by the ID Card give the message "You need an id badge". This is because the positions of the ID Card and ID Badge are switched in the key list enum compared to the global mobj table enum: the badge is the 137th mobj defined, which makes it the fourth key (the first, the base key, being 134th overall), and the card is the 11th key (144th mobj). But in the key enum, the card is in fourth position while the badge is in eleventh position.