Seems like a glitch that wasn't realized. An event was set to proceed in the game, but the events weren't active because you lost and left the ship. You may have to reset before the aircraft, if you have a save there. If not, you may not be able to do it.
I know when you go to Breeze Island, you have to go to Team Earth's building and that's where you start the good/bad part of the game. If you go on the aircraft, look for the hole in the wall near the end. You have to exit out through there and talk to the two Dark Organization grunts in the woods.