*attempts to wade back into the fray* Hopefully this will help. It's my personal view since I'm trying to... make sense of things myself.
I choose to believe one of two views:
A. Harlock found the 'cause' he was looking to lay his life down for and died (Which I really choose not to think)
or more likely
B. Harlock being the stubborn bastard that he is, was shot and didn't die. I seriously doubt that the man could. Seriously. It would be far too easy for his whole character to give up, even though he DOES have a little bit of a suicidal streak.
Either way, the Arcadia picked the crew up from New Terra, and dropped Tadashi off to start his life as a Man. Harlock wasn't guiding it from the inside. Hell, the ship itself is alive. Tochiro's spirit lives in the CPU, and there IS a wheel at the top of the bridge.. turret? Is that the right word I want? *points to the opening of SSX and the GE999 movies* He IS on the outside of the ship with the rest of the crew watching Tadashi walk away.
I suppose Harlock did the Harlock thing: Pitch everyone off ship to live their lives and leave.
What perplexed me the most was that Tochiro was on the ship with his daughter, Mayu. But then again, Matsumoto was never one for continuity, which suits me just fine. Adds a bit of intrest to the whole piece.
Hope that helps some to clear things up...
I believe option "B" is more likely than any other theory...Or maybe they decided to don't shoot eachother because,after all,they are friends and to hell with vengeance,promises and such ;)
But the greatest mystery is yet to be solved...If that kid with Tochiro is Earth's personification,where the hell is the true Mayu??
Thankyou to you both!