Galaxy Express 999 is a story in its own right, with its own cast of central characters, but Harlock and company do occasionally show up for a bit of fun, and cause all sorts of exciting confusion.
What's the prob, Bob? Well, for starters, the Captain Harlock series is set in the year 2977, and Galaxy Express 999 is set in 2221. Despite this, Harlock, Tochiro, and Emeraldas all make appearances in both stories. Maybe this isn't such a big problem. Perhaps, one might surmise, in the future everyone lives forever. But then one must ask just what the allure of an immortal machine body would be in such a world, and must then toss the idea aside as unrepentantly silly. Matsumoto could've simply set both in the same general time frame; after all, it's not as if the technology depicted in Space Pirate is much different than that in 999. But of course, he didn't. This is what is known in literary circles as "not giving a damn." The stories supposedly overlap, the time frame makes it flatly impossible, and Matsumoto doesn't give a damn. He's going to write down the first thing that comes into his silly little head, he'll stick a square peg into a round hole and ignore the fact that it didn't really go in there at all, and have a good laugh at your expense when you don't understand it. He doesn't give a damn. So neither should you.
The first 999 movie is the first time we see Harlock and crew subsequent to the first series. "But wait," you're probably saying, "surely he was seen in the 999 TV series before that, right?" One would be tempted to think such a thing, but one would be wrong. At 113 episodes, Galaxy Express 999 ran so damn long that the film actually came out long before the series completed its run, a fact which probably spoiled the outcome of the series for quite a great many viewers. So while Harlock does appear in the TV series-albeit in the most infuriatingly enigmatic fashion ever-it wouldn't be until after the movie had already come along and made a mess of the still-fledgling continuity.
The 1979 Galaxy Express 999 feature introduced audiences to the now-famous green, skull-prowed Arcadia, which Bandai had designed so they could sell their own plastic model kits of the pirate ship instead of inadvertently advertising the blue Arcadia model kits produced by their rival Takara. (Yep, the Space Pirate series was also still running at the time the 999 feature hit theaters.) The crew seen in the feature was the same crew as seen in the Space Pirate series, minus Tadashi Daiba. This might lead some to assume that the film occurs before the events of the Harlock series (given the dates of the respective stories, one would assume nearly 800 years before.) However, the film also gives us a brand-new version of the death of Tochiro Oyama, one which bears no similarity to the one seen in the Harlock TV series. (The computer can speak with Tochiro's voice in this version, instead of creaking and groaning as it did previously.) We also see Emeraldas now sporting her Harlock-style scar, and commanding the zeppelin-galleon combo spacecraft that would appear in all future versions. Much of the action would occur on planet Heavy Meldar, which had been previously seen to do the big firework in Space Pirate episode 31.
Harlock finally made his, ahem "appearance" in the 999 series in the three-part episode "Pirate of the Time Castle" (episodes 79-81.) The Count Mecha character, who had played the role of major villain in the film version, had been killed off in the very first episode of the TV series, so the Time Castle would now be seen to be ruled by, apparently, Harlock himself. Believing he has betrayed her trust, Maeter has come to the again-resurrected Heavy Meldar to kill him, only to find that she's actually facing a mechanical Harlock imposter. The real Harlock spends the whole story wrapped in a dark cloak, the only clues to his identity being his voice and the gleam from his eye. At the close, having been apparently content to let Tetsuro and Maeter do all the dirty work, he blasts off in the Arcadia-the blue Arcadia-once more, without ever showing his face one single time.
In an interesting bit of restructuring, the character of Ryuze from the 999 series also appeared in the film version as the consort to Count Mecha. In the series, she had been seen as a time-controlling witch who was bitter at pretty much the whole universe after being spurned by the otherwise-unnamed "Baron." The Pirate of the Time Castle story bridged the gap by introducing Ryuze's sister LeRyuze, who was modeled on the 999 film version of Ryuze, in order to fill the role.
Everybody getting this so far?
The 1981 Adieu, Galaxy Express 999 film picked up two years after the first film left off, and in the process of depicting the fall of the Mechanization Empire, introduced the character of Faust, the Black Knight, Tetsuro's father and an old friend of Harlock's. Beyond this film, Faust's origins were never explored, though the Endless Road SSX series was originally supposed to deal with this (its premature cancellation may have had something to do with why it didn't.) The film concludes by stating that Maeter departed, "never to be seen again," but 'never' is a rather relative term in these circles.
In the end, it would be seventeen years before Galaxy Express 999 made its return, in the form of the 55 minute theatrical feature Eternal Fantasy, based upon Matsumoto's new 999 manga series. Interestingly, it seems to work equally well as a continuation of either the series or the two previous features, provided one ignores that "never to be seen again" bit from Adieu, since Maeter does indeed return. The feature introduced the Metanoids, metallic creatures who would also be seen in the Queen Emeraldas OVA series, and would also be the first occasion on which voice actor Makio Inoue would not provide the voice of Harlock. Harlock would be voiced by Koichi Yamadera for all future appearances of the character (to date.) Yamadera would also provide the voice of Tochiro, whose original voice actor, Kei Tomiyama, had died in 1995. The feature ends with the story left hanging, and supposedly there was to be a full-length theatrical feature that would continue and conclude the 999 story once and forever (of course, it had already been concluded once.) However, this sequel film has yet to see the light of day, and we may never be let in on why the Yamato makes a sudden, unexplained appearance at the end of the film (well, you know, unless we read the manga version,) or what happens after the earth does the big kaboom. Oh crap, did I spoil the ending?
As for linking 999 in with the Queen Emeraldas OVAs, well, take a wild guess. Queen Emeraldas episode two was the first place that we heard of this new notion that Maeter and Emeraldas were sisters, an idea which flies totally in the face of the backstory already established in 999--Queen Promecium refers to Maeter as her "only daughter." The first episode also includes a scene of Tochiro and Emeraldas in a huge hangar containing the Queen Emeraldas, the Deathshadow, and the Yamato, the presence of which is never explained or even mentioned. Tochiro is at this point planning to build the Arcadia--we see a scale model of it, and it's the green one--and yet in the fourth episode, there's a flashback showing the blue Arcadia (now painted black, but it's the same design,) and a new explanation for Emeraldas' scar that contradicts the version we saw decades ago in My Youth in Arcadia (it's now a sword-wound caused by the Siren Goddess, who is, in turn, utterly unconnected with the Siren Witch from Adieu, Galaxy Express 999. There will be a quiz later, so keep up.) So basically, no, it doesn't work. It pretends to, but like Richard Nixon, it's a bad liar, though not nearly so much as the two-part Maetel(sic) Legend OVA, which scribbles all the hell over the origins of Maeter, Emeraldas, Queen Promecium, Count Mecha, and the Mechanization Empire whilst being totally dull in doing so.
And yet, there are, to this very day, folks that insist that all these stories can be put into some proper, cohesive order. What sort of drugs these people are on is beyond me, and furthermore, the stingy bastards aren't sharing.