Capcom makes some great video games, but most of the time they can't tell a long term story. Sequels contradict other games in the series, turning years worth of storyline into a muddled mess. Consider the many faces of Mega Man, for example. It is known and accepted that Mega Man X takes place years after the original Mega Man series, while Mega Man Zero takes place years after Mega Man X. The question is: how do Mega Man Legends and Mega Man Battle Network fit into things?
Fortunately for us there are people out there who do this kind of heavy thinking and research. People such as Miranda Paugh of The Mega Man Homepage. She's thought long and hard about how the entire family of Mega Man titles fits together in one neat little package.
The Legends series could be the far future of the X series, after some catastrophic event flooded most of the world. (Given what goes on in the X series world, this wouldn't be very far-fetched.) The technology in the Zero series (which takes place about 100 years after the X series) is starting to resemble the ancient technology that you can dig up in the Legends series, so it's possible that Legends takes place sometime after the Zero games. (There still aren't really any Reaverbots in the Zero series games, but I suppose we just need to give them time.)
The links are tenuous at best, but do provoke a little thought. I got off the Mega Man train when the X series started to run out of gas so I'm not as familiar with the exploits of the other Mega Mans, but after reading this explanation I have to say that I am just as confused as before, yet smarter somehow. Ain't the Internet grand?