In Crisis Zone, the player controls the elite anti-terrorist Special Tactical Force (STF) leader, Claude McGarren.

The game uses the same pedal system to reload and hide; however, the player uses a machine gun, a customized Heckler & Koch MP5K with a sight laser and a capacity of 40 rounds.

The "crisis flash" is replaced with a warning target icon to remind players to hide from a threatening shot, though it is possible to interrupt the enemy from shooting.

With an unknown threat, Scotland Yard and MI6 dispatch the Special Tactical Force's (STF) First Platoon Unit (led by Claude McGarren, spelled as Croad Macgalain in the arcade version) to suppress the URDA, and to ensure that the terrorists don't access their hidden agenda, whatever it may be.

Making their way down to the control room, five kilometres below the complex, McGarren and his men defeat Lynch's troops before taking out the ringleader himself.

Six months after the main story's events, Lynch's successor Jared Hunter launches another attack, seizing control of the Grassmarket District and holding STF Director Grant Kessler's daughter Melissa as a hostage.

Declaring his intent for revenge, Hunter engages and loses to Squad 1, forcing him to retreat on a modified, heavily armed speedboat, but is killed when the boat is destroyed by McGarren's chopper.