The Scientist has taken over GLOBEX and has brainwashed the original Strike Force Heroes after capturing them in the second game (except General West, who was murdered by Dex) and Strike Force Command wants Wesley (the first player character and assumed to be the "Rookie" mentioned in SFH2) to rebuild the squad and stop your former allies before they help GLOBEX take over the world with their clone army. In the end, the original Strike Force Heroes are defeated and the clone army's rampage is stopped. The Scientist, furious at the failure of his plans, massacres his entire staff and proclaims that he will succeed where his predecessor had failed by destroying the SFH once and for all. Meanwhile, back in SFH base, Wesley gets an unexpected message from a very much alive GLOBEX Leader...