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, jungles that 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.