The humans plan a last-ditch attempt to destroy 'The Skulls', but their first priority is to secure Planet Anubis, where the miners have discovered something in the mine shafts. No survivors are found, but the player is sent to destroy the mine shafts and whatever may be in there. The player soon discovers that 'The Skulls' were living underground, but sick and tired of constant threat by the miners, they set out to eradicate all humans from existence. But while moving through the mine shafts, the player falls deep into the Skulls' lair. The player first meets a 'Queen' in this level, and after defeating it, the CDF find and evacuate the player. They prepare to send the player's team onto the enemy's current stronghold, the Juggernaut, but are ambushed along the way.