Metal Slug 3

Several years ago, the evil General Morden was foiled in his attempted coup d'état against the worlds' governments by the Peregrine Falcon Strike Force. After forming an alliance with an alien race in an attempt to stage another coup, Morden was betrayed and taken prisoner by his newfound allies. His rebels troops formed an ad hoc alliance with the Strike Force and the aliens were defeated and Morden was killed. Instrumental in defeating Morden during the first coup were Cpt. Marco Rossi and Lt. Tarma Roving. Rossi (now a Major) and Roving (now a captain) led the fight against the Morden during the second coup, joined by two members of the Intelligence Agency's Special Ops Squad S.P.A.R.R.O.W.S.; Sgt. Eri Kasamoto and Sgt. 1st Class Fiolina Germi.
Several years have passed since that time, and Morden is listed as missing by his surviving followers. Determined to wipe out every remnant of Morden's powerbase, the army send Rossi and Roving to destroy all remaining rebel strongholds, one by one. During the fighting, however, Rossi and Roving come to the conclusion that the enemy is too well organised, and perhaps Morden is not dead as was initially thought. Meanwhile, the S.P.A.R.R.O.W.S. come across a series of strange events which lead the army to conclude that the aliens with whom Morden once allied himself have returned.
The Peregrine Falcon Strike Force and S.P.A.R.R.O.W.S. are once again united, and sent to defeat this new threat. After various battles against Morden's forces, the heroes face off against Morden. After defeating him, it is revealed that it was an alien in disguise, and the real Morden has been taken prisoner by the aliens. The aliens abduct the player character and leave Earth. At this point, another character takes the player character's place. An ad hoc alliance is formed between the Strike Force and Morden's troops so as to save their captured comrades. The rebels launch an armada of rocket ships to attack the alien mother ship, Rugname. After a long battle through the ship's interior, the Rugname starts to collapse due to the amount of damage it has sustained. After destroying the ship's core, the Strike Force must fight their way through armies of clones of their captured teammate, some of whom have turned into zombies. Both the captured member of the Strike Force and Morden are freed. As they escape, they are confronted by the aliens' leader, Rootmars. A battle ensues in Earth's atmosphere, which is won by the Strike Force, who leave Rootmars' body in the ocean. Upon seeing Morden and his men celebrating, the player character throws their weapon into the water in disgust.