Basically, you have the original continuity, which is the classic series (Bass's canon), X series (X and Zero's canon), Zero series (X and Zero will end up here someday if DDD goes on for hundreds of years), and ZX series (Giro and Grey's canon). They're separated by pretty wide gaps (they're all in different centuries), and there are storyline connections of roughly increasing strength--the X series has only a vague relation to the classic series, while the ZX games' plots are basically one big reference to the Zero series. There's also Mega Man Legends, which is purportedly in the waaaay distant future of this timeline and basically has no connection to it whatsoever. All of these (I think) have manga associated with them, none of which have come into play here at DDD besides being mined for icons. There was also an American-made cartoon based loosely on the classic series, which is Protoman's canon (there was a Protoman in the actual classic series, but about the only thing they have in common is their appearance and being Mega Man's "brother").
Then there's the MegaMan Battle Network series, which, again, has the Mega Man Star Force series in its distant future. This universe has no connection to the first one, though a huge number of characters are based on classic-series or sometimes X-series characters. MMBN has a manga and anime associated with it, which are known as "MegaMan NT Warrior" in English. This is Lan and MegaMan.exe's canon.
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Basically, you have the original continuity, which is the classic series (Bass's canon), X series (X and Zero's canon), Zero series (X and Zero will end up here someday if DDD goes on for hundreds of years), and ZX series (Giro and Grey's canon). They're separated by pretty wide gaps (they're all in different centuries), and there are storyline connections of roughly increasing strength--the X series has only a vague relation to the classic series, while the ZX games' plots are basically one big reference to the Zero series. There's also Mega Man Legends, which is purportedly in the waaaay distant future of this timeline and basically has no connection to it whatsoever. All of these (I think) have manga associated with them, none of which have come into play here at DDD besides being mined for icons. There was also an American-made cartoon based loosely on the classic series, which is Protoman's canon (there was a Protoman in the actual classic series, but about the only thing they have in common is their appearance and being Mega Man's "brother").
Then there's the MegaMan Battle Network series, which, again, has the Mega Man Star Force series in its distant future. This universe has no connection to the first one, though a huge number of characters are based on classic-series or sometimes X-series characters. MMBN has a manga and anime associated with it, which are known as "MegaMan NT Warrior" in English. This is Lan and MegaMan.exe's canon.
Confused yet?