According to the player's unseen commander, a bioweapons research facility on the continent has been taken over by the terrorists and its staff held hostage, including Laura, one of the scientists whom Falcon had recently been dating (and whom he finds out is also the sister of his counterpart).

The player is then sent to the research facility, and kills several snow based enemies.

After completing the snow missions, the player is sent to recover a stolen airplane, and afterwards, faces another boss, Cobra, who seemed to have survived the previous encounter in Silent Scope and claims to be immortal.

The boss, The Collector, is more challenging than the previous ones, as he has full body armor and has a tank as well as several fire arms as weapons.

Finally, the player is sent to the enemy's base and battles a pair of ninja-like bosses, Sho and Kane, before facing the big boss, who is on a top of a clock tower with Laura as his prisoner.