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okay, finally won this fight (after an insane amount of times).
However I'm stuck again! :-D
(this time for real I'm afraid)

I'm currently at Station Sigma, after getting locked in the save room and now in the room where the cutscene plays.
The girls tells me to choose whichever door I want.
However only 2 doors are accessible without the bat around and both are "not ready yet" and I should come later.

Did I find the end of the game? O_o

Doubt that but I don't see any way to leave the room.
Or am I supposed to wait and the other bat will eventually return, giving me a chance to escape?

You've found AN end of the game, that's correct :3

I don't quite remember everything that's accessible, but if I remember correctly... working with Bass lets you reach an area called the Deep Cave. Just exploring the path towards the bottom of the mountain (getting as far down as possible in the village, then get to another outside section, then further down) lets you get to an area called something along the line of "Abandoned Construction Site", though I probably used a different wording. Both of those lets you progress down different story paths.

Yeah, that's true. After the suntown thing, I was given the choice wehter to lie to the bat king (that Bass kidnapped her before we arrived) or to follow Bass to Deep cave or whatever it was called.

Since I didn't know where Deep Cave is , I went to the last thing I rememberred that was relevant for the quest:
The bat king guy.
Everything after that more or less followed a straight path.

So searching for the deep cave would have lead me to other endings?
Damn it, getting back through that insane amount of enemies without that other girl is impossible, so that's it I guess.

Althoug I regret that I still haven't gotten all the weapons to destroy the different blocks , for example the dragon martial arts skill from the central cave area. :-/

If I remember correctly, once Bass teleports away and leaves his base in the Central Cave unattended, you can search his stuff for a note with teleporter coordinates to the Deep Cave. Going to the base teleporter once you've found that should unlock the Deep Cave as a warp point.