While the film is busy educating viewers on the importance of looking after the environment, particularly marine life, a crafty alien spaceship slips into the ocean. Such sass and irony! It threatens mankind in a notable ‘shoe on the other foot’ kind of way, but the flying chelonian hero is soon on the case, selflessly fighting for the survival of all mankind.
Although not commented upon directly, if you use your noggin you can figure out a legitimate reason why the invading alien presence knows how to speak fluent Japanese. That's called progress, folks.