The campaign in Lost Planet 2 is divided in six episodes, picking up ten years after the events of Lost Planet: Extreme Condition. The episodes put the player in different environments all around E.D.N. III, where he becomes part of a snow pirate colony and takes part in the story surrounding the climatic change of the planet.
The effects of the improved Frontier Project on the planet makes the revived plants grow at an accelerated rate. Dense flora now covers the Amuraba sector.
A squad of Snow Pirate Mercenaries are sent into the Amuraba Jungle to attack a Jungle Pirate mining site. They face a hard fight in and out of the jungle through especially hostile Akrid and angry Jungle Pirates. When their rendezvous point turns out to be the lair of a Category-G Akrid, they realise that the job was a setup- but who would take the time to set up such a complex trap just to kill off a few mercenaries?
A NEVEC Black Ops Team called "Task Force First Descent" is dispatched to infiltrate Central City and destroy a new superweapon developed by the Carpetbaggers. The battle hardened team of clones sneaks through the city at night, battling sentries and Vital Suits until they reach the Railway Gun. The weapon makes its escape when a Category-G Akrid shows up, leaving Task Force First Descent to stop it. Upon killing the Akrid, the squad receives new intel about the mysterious Over-G that threatens the entire planet and is redeployed to investigate the Over-G. As they walk away from the city, it is revealed that they are the clones of Ivan Solotov- the man who betrays NEVEC. An NEVEC field commander states frankly that sending them to suicidal missions is to get rid of them and consequently taking off a burden from NEVEC.
The Waysiders roll through the desert on their train, worn out after a botched raid on the Carpetbaggers, only to be attacked by the monstrous "Red Eye". From one train to another, and then another, the Waysiders fight their way back on course and take control of the Railway Gun, just in time to deal with Red-Eye once again. After fending it off, they expect to receive a heroes' welcome when they return home- instead, they find that the Over-G's snowstorms have utterly destroyed their town. With nothing left to lose, they set a course for the Over-G.
The ex-NEVEC forces step into motion. They have to prevent NEVEC from proceeding with their plans for the newly awoken Over-G akrid, and save the lives of everyone on E.D.N. III. First they have some loose ends to tie up, then it's time to suit up for space. There's a shuttle headed for the NEOS space station, and the ex-NEVEC team has to get aboard and infiltrate NEOS Space Station and gain control of the Orbital Cannon. After rescuing part of their squad from a Carpetbagger prison, the ex-NEVEC team infiltrates the shuttle launch complex, destroying NEVEC's experimental weapon "VF" just in time to sneak on to the last shuttle to NEOS.
It's fiesta time for the Vagabundos as they gleefully raid NEVEC's new Overland Battleship. They get to fight the carrier's personel, a huge Cat-G and then another Overland Battleship as well. It's true pirate glory until they catch sight of the Over-G akrid on the horizon. Where most other men see fear and danger, these desert dwelling bandits see fortune and glory!
The ex-NEVEC team has made it to NEOS, but they still have to get inside it and gain control of the orbital cannon's systems. With some help from First Descent, they get the job done, and it's on to the next phase. The Over-G akrid must be destroyed before it's too late, and it's going to take every last man to get it done. The ex-NEVEC leader calls out to the Snow Pirates of E.D.N. III for aide. For the honor of their ancestors, for the future of their children and for their own glory, they answer the call to arms. The final battle takes place on the Over-G's mountainous body. To prevent it from absorbing too much amount of energy and freezing the planet solid, the ex-NEVEC team must work with the men on NEOS and their newfound Snow Pirate allies to bring the Over-G down.