The story takes place back on E.D.N. III 10 years after the events of the first game. The snow has melted to reveal deserts; and jungles have taken the place of more frozen regions. The plot begins with mercenaries fighting against jungle pirates. After destroying a mine, the mercenaries continue on to evacuate the area, in which a Category-G Akrid appears and attacks them. After being rescued, they find out their evacuation point (where the Category-G appeared) was a set-up and no pick up team awaited them.
The game then shifts to NEVEC's Black Ops, Task Force First Descent, who fight their way through a Carpetbagger city in an effort to capture a railway gun, a train mounted with a massive cannon. After failing to succeed, a "space Akrid" appears and begins to attack the group. After it is killed and the members evacuated, it is revealed they are clones of Ivan Solotov, a character from Lost Planet: Extreme Condition.
The story once again shifts, this time to Waysiders, snow pirates now living in the desert. They are returning from a raid on a carpetbagger city, apparently with heavy casualties and not much thermal energy. On the way back home, they are ambushed by a Category-G Akrid, dubbed "Red Eye".
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