The player controls Lieutenant Jack Morton of NATO, the sole survivor of a terrorist strike on the Blue Harvest, an armored train. He is aided by Christina Wayborn throughout the game, the French ambassador's bodyguard and the NATO council. Traveling around the various carriages of the train, the player must defeat the terrorists, find the French ambassador, and prevent the terrorists from using a nuclear weapon.

The terrorists, under the leadership of Boris Zugoski, detonate some C4 charges in parts of the train, kill all those who resist and take the French ambassador's family hostage. At a certain point in the game Boris is killed by Jack and it appears that the ambassador's assistant, Phillip Mason, is actually a double agent sent to steal a data disk from the Blue Harvest.

The ending depends upon what data disk the player gave Mason.

Good endings consist of Mason attempting to escape in the helicopter but being stopped by Jack who stops the nuclear bombs on board. The Ambassador is saved as is Billy.

Bad endings consist of Mason escaping and remaining at large. Jack then stops the nuclear bombs however the Ambassador dies as does Billy.