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It starts with the squad stopping a rebellion. On the way back to their base they are attacked by unknown forces. They are forced to land on a mysterious island. Once they land many of the squad succumb to a unknown illness and go on a rampage. The player is the only survivor. He happens upon a facility where he finds a scientist under attack from the same guys who attacked his squad. The scientist explains about the incident and the virus that enrages people. They receive backup and start helping the scientist develop a cure. In the meantime they learn that the group who attacked them is a grou​Zp called Globex. Globex attempts to destroy the facility in order to keep the Heroes from getting the information about the virus. When this fails, they plan to launch a nuclear missile to destroy the island. They launch it, but the heroes are able to intercept the missile and replace the warhead with the cure instead. After a final battle it is assumed that Globex is done. However, some time later an orbital satelight station comes under attack. At the same time the Bravo squad of the Heroes are initiating a new recruit. Their base is infiltrated by Globex. The Heroes locate the scientist and discover that the soldiers are all clones. They help the scientist gather materials. A mercenary in the group raises suspicions on  the General, who has been acting shady recently. It is later revealed that the merc had sold them out.