After the original series, on the second arcade game it is stated that Wily builds Zero, and it has his blue prints in the background. Dr.Wily told Bass that he used something by accident when creating Bass called Bassnly (i think thats what its called)and used the program to make zero, and told Bass that this person will be stronger than Megaman and him combined. Bass swore that when this person awoke he will defeat him, along with Megaman, because of his personality he couldn't see the reality of the situation.
Protoman, being the first built robot every, had a special kind of unknown sickness, and Dr.Light confronts him about it. Protoman is a lone wolf guardian angle type person, he tell Dr.Light that if he cant take care of himself, then no one should be able to. So he leaves, and dies of the sickness many years later.
When all of this is going on, Dr.Light was secretly designing a new kind of Robots called "Reploids". These robots would be more 'human' like, and could think for themselfs. Fearing that the world isn't ready for that kind of jump in robotic technology, he kept the latest model MegamanX a secret from the world. Megaman X was the first Reploid.
(I use my theories with hard evidence and soft evidence of the games, these are not fact)
Theory: 1) The laws of "I Robot" for Robots where in effect in the entire game, as shown on the end of Megaman7, Megaman states that he's a human before he's about to attempt to kill Dr.Wily for putting him through so much stress, but unfortunately Bass stops him. my first theory to the original Megaman Dieing is that he became out of control, the laws that he was programed with contradicted itself, and Dr.Light had to put him down.
2) Zero awoke and killed Bass, and killed the original megaman, Wily probably lost control of Zero, because he was too F***ing powerful (and the time you see him in this original state on Megaman X4, it shows him out of control, that was his original personality!) Fact: Zero was out of control, Zero was the first Maverick. back to Theory: Wily sealed him away to awaken many years later (over 100 actually).
21XX-X's story (I'll continue this in a bit.....)
One hundred years later, Humanity was a little weak without Robots, and they where slowly dieing off because of Dr.Light not being alive anymore.
A Scientist (and soon leader of a special squad called "The Maverick Hunters/ Irregular Hunters) named Dr.Cain stumbled upon a old laboratory, happen to be Dr.Lights old laboratory, and its been abandoned for a VERY long time. He searches the lab and finds a mysterious robot named "Megaman X" and a transmission from Light appears, as light tells one of his final words, barely being able to talk almost, he basically states that Megaman X is the next type of Robotic technology called Reploids, and he designed it a few years too early, and thought that the current time that he was in wouldn't accept a Robot that could think for itself, be a little more human like in the looks, and in the actions. He felt that the laws of robots being held back made them un-alive, and also told who ever found X that "X" was a variable, the potential to be the greatest robotic to ever be built, but only time would tell of his potential power, and if he even WANTS to fight.
Dr.Cain took X and created similar like Robots called Reploids and mass produced them around the world, the time period was perfect for it, but where there is good, there is evil. Some Reploids where going rouge, and attacking innocent humans, these Reploids where called Mavericks. A few weeks/months later a mysterious Red Reploid was seen in a factory, and he was out of control, the current leaders of the Maverick hunters, Sigma, confronted him and they fought and Sigma barely won by punching Zero in the Crystal on his forehead that shined a big "W". This caused Zero to loose his memory.
some time later, X decided that he wanted to help people, and had a high since of justice, he joined to become a Maverick Hunter of the 17th unit. Zero, who lost his memory, and had a 'get the job done' personality that day forward, basically went "What the hell, I'll fight for justice cause mavericks make me sick". He joined to kick some ass, and became apart of the 14th unit (I might have the Units backwards, or completely incorrect, I'll look them up now, but i need to go for a bit.., I'll continue this in a sec.)