Super Robot Taisen OG GBA Kyosuke Mission 14 Help *Poss Spoi

Alright ive already looked on the faqs of game, and tried looking on the net but I cant seem to find the answer I seek. During this mission you have to stop the peregrine with the president on board. I get him on the third turn, and the ship is supposed to become an npc (turning yellow I think) but mine stays red, and after I kill all other enemies, its still red, so I try attacking it, and all I can do is kill it, and then I get a game over. Ive tried it like 5 times now, and it still does the same thing. Is it possible this copy of my game is also screwed up? Should I restart this storyline? Not sure what to do and even Atlus's forums dont have any info. Any help would be appreciated. Thanks.