You're going down... again. If you thought Descent went to the edge of 360° 3D power-blasting sensory insanity, then prepare yourself. You're about to plunge over the edge, and into the depths of Descent II. Suddenly warped into the outer reaches of the Zeta Aquilae System, your new mission sends you into the black depths of treacherous alien mines. You blast through enemy robots with powerful new tools, leaving their flaming hulks in your exhaust. Your ultimate goal: to exterminate the alien robot stronghold from the enemy Alien Base and claim total control -- it's 30 new levels of outrageous destruction. But this time, you're not alone. Joining you on your deadly new assignment is your loyal Guide-bot. This faithful companion rushes with you through the twists and turns of the menacing darkness, often scouting ahead to hunt down the orbs, powerups and tools you desperately need to complete your job. But beware -- raging enemies are still determined to destroy you, including the menacing Thief-bot who's set on stealing your weapons of destruction and precious powerups. Get ready -- Descent II is about to take you on a whole new synapse-smashing ride.

The plot is linear and is mostly provided for the introductory and concluding full-motion video cutscenes. After the "Material Defender" (voiced by George DelHoyo) has destroyed all of the Solar System's mines in the original game, he stops in the asteroid belt to dock. He is then contacted by Post-Terran Mining Corporation executive Dravis, who exploits a loophole in a contract to coerce him to accept a new mission or forfeit his reward and face legal action. The Material Defender consents, and as Dravis tries to convince him that he is merely embarking on a reconnaissance mission, his ship is fitted with a prototype warp core. He is then sent to clear out PTMC's deep space mines beyond the Solar System. The Material Defender teleports to Zeta Aquilae and five other, fictional star systems and destroys their mines. In the sixth system, the last mine seems to run all through a planetoid, which is revealed in the final cutscene to be a large spaceship. After the spaceship breaks apart, the Material Defender alerts Dravis to his return home, but his warp drive malfunctions and he teleports to an unknown location. The camera then fades to that location and the ship appears, heavily damaged and crackling with excess radiation drifting towards the camera, ending with the words "to be continued..." being displayed.