What the hekkie happened at the end? Spoilers obviously.

I don't normally have any problems following convoluted plots and generally prefer movies that have a lot going on. I can't for the life of me figure out what happened at the end of Harlock though and I can't find anything online that seems to understand either.

So everyone died, including the alien, it looked like they were setting up for Harlock to die and be replaced by whatever his bland name was, which is fine whatever Davy Jones never ending ghost ship analogy blah blah blah.

But then Harlock didn't die, and somehow the ship starts running again and has it's deus ex machina dark matter back even though they said it was out and the dead alien is back and now everyone accepts the bland kid as the new captain even though their freaking captain is still alive, sitting behind him. There doesn't even seem to be any sane reason why this kid has to be the new captain, because it was never really established that this ship has to keep running forever, and they had just said that it was done for.

I feel like either I missed something very important, or the most incompetent writing in history was meticulously, and beautifully rendered.