There is one persistent question that is repeatedly asked regarding the character of Captain Harlock, and, after viewing the Arcadia movie, one which will generally be asked again in a slightly modified form. These questions are, respectively, "How did he lose his eye and get that scar on his face?" and "No, really, how did he get that scar, and why do his ancestors have the exact same scar?"
The first question is almost irrelevant, as the only real way to answer it would be "Somehow. Who cares?" A disfigured hero is an iconic image passed down through generations of dramatic tales, and scarcely needs a specific explanation. The second question has much more significance, and it is almost always answered by the proclamation "Because it's actually genetic, and not a real scar."
This is, of course, preposterously silly.
There are so many things wrong with this so-called "explanation" I can barely decide where to begin. How about the fact that while certain medical conditions that can lead to birthmarks can be inherited, specific birthmarks are not inheritable; there is no "birthmark gene" that could cause the same shaped-and-placed mark to appear repeatedly over the course of generations. Birthmarks are deformities caused by mutated cells that develop in utero, and there's consequently about as much chance of such a specific and complex shape appearing on the faces of multiple family members over even one generation as there is of finding two identical snowflakes lying side-by-side. Two or even three members of the same family all accidentally acquiring scars in the same spot would be infinitely more probable.
Of course, this sort of smarmy "I know more about science than you" approach is somewhat like squashing a bug with a sixteen-ton weight. There are far more basic observations which can be made, such as the fact that these sorts of attempts at explanation take a basic "tunnel-vision" approach with regards to the scar. One might just as easily ask why Harlock's ancestors precisely resemble him in every other respect. One thousand years later, and Harlock still has the same facial structure, the same build, the same voice, the same hairstyle, and even the same personality as his twentieth-century predecessors. It also appears that Phantom F. Harlock Senior is even missing the same eye; are we to gather that the Harlocks have some sort of genetic predisposition to getting their eyes shot out? One would hope that basic Darwinian mechanics would weed out such a potentially hazardous trait over time. Plus, we must realize that these same observations apply to Tochiro, as well. His World War II-era ancestor sports the same face, same stature, same voice, same first name, same profession, same need for eyeglasses, and same ambition (space travel) as the Tochiro of the future, and like his descendant, he becomes a functioning part of a craft named "Arcadia," piloted by Harlock. Genetics are indeed a weird, wacky thing.
For me, however, the best argument against the "birthmark" theory is the simplest one: it's boring. Our swashbuckling, grim, determined, odds-defying bucker of the system might as well have been a snivelling, rat-faced coward; he still would've had that bitchin' scar. Reducing it to a simple physical deformity strips it of all its iconic power: it no longer symbolizes the price of fighting the good fight and living on one's own terms. As a birthmark, it symbolizes nothing at all. He might as well ask Dr. Zero to put down his bottle just long enough to remove that potentially cancer-ridden pink centipede from his mug. As an actual injury, however, it represents sacrifice. This is most obvious in the case of Emeraldas, who first appears, scar-free, in the Arcadia film as one who is, in her own words, "no one's enemy, and no one's ally." When she decides to back Harlock and the Tokargans in their struggle, she is shortly thereafter rewarded with the exact same scar as Harlock. The bandit Antales from Galaxy Express 999 also bears this scar, and Zoll of Tokarga (as he appears in the Space Pirate series) has multiple scars across his head and face. However you try to rationalize it, scars on Matsumoto heroes are emblems of the cost of freedom and defiance, a fact which comes across again and again.
Any other interpretation of Harlock's scar seems to result from the desperate attempts by sci-fi fanatics to shove some (rather poor) semblance of science somewhere it was never supposed to be in the first place. His real-life passion for astronomy aside, Matsumoto's stories show so little regard for the facts of science that his characters often don't even bother with spacesuits when slipping outside their ships. What we see in Arcadia is simply a rather vaguely science-fictionalized (vaguely in that it involves no actual science) interpretation of the notion of reincarnation, a fact which was undoubtedly far more obvious to the film's originally intended audience. We see two personalities meet and bond over common ideals, but the time is not yet right, and circumstances prevent their dreams from coming to fruition. A thousand years later, these two souls meet once again, and this time come together to fight for their mutual goals and beliefs, continuing to play out the same drama and face the same obstacles. One of the many strengths of fiction is its ability to go where reality cannot, and to explore those ideas that have tantalized the imaginations of humankind throughout the ages, but which are more a result of the manner by which our minds work than they are of anything factual. (There is, I should point out, a great deal of psuedoscientific prattling on the alleged connection between birthmarks and reincarnation, dispensed by those who obsessively need to find the answers to the universe hidden within random happenings that require no explanation. I unapologetically call this lot a bunch of silly sods.)
Captain Harlock and his antecedents have scars because, at some unwritten point in their lives, they earned them. Captain Harlock simply is Phantom F. Harlock, still fighting to acheive his dreams. Apply reason to real life in heaping quantities, but allow speculative fantasy room to breathe.