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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.
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." After loading the remaining Thermal Energy on helicopter like VSs, they make their escape, only to be shot down by sandraiders. After stealing a train from the sandraiders, the group is ambushed by Carpetbaggers on the railway gun. After seizing control of the gun, they are once again attacked by Red Eye, this time they are able to kill it though. As they continue towards their home, it starts snowing heavily, burying their home. The player 1 waysider notices a giant, glowing orb in the distance and declares "I'm so going to shoot the shit out of you!" and apparently fires at it.

The game shifts to two NEVEC people talking on a helicopter VS. The orb seen by the waysiders is declared "the Over G", and its increase in thermal energy use will trigger another ice age on E.D.N. III. NEVEC plans to kill it with the satellite known as NEOS. Once the thermal energy is harvested, they will abandon the planet. To prevent this genocide, most NEVEC ground troops defect. Two Ex-NEVEC characters are imprisoned by Carpetbaggers, but are freed by one who "Brought your friends here." More Ex-NEVEC troops rescue them and they make their way through the underground tunnels. They capture a NEVEC submarine and make their escape. Meeting up with all the other Ex-NEVEC troops, an invasion of a NEVEC base is planned. The base is captured and an experimental weapon created by NEVEC is destroyed. The group of player troops stowaway on a shuttle headed for the space station NEOS. The plan is to use its massive firepower to destroy the Over-G before it reaches its final form. The plot shifts quickly to the "Vagabundos," A group of sand pirates. They battle NEVEC troops, eventually capturing a massive gun from NEVEC. They see the Over-G in the distance and decide to head there.