We all get the fact that Zero begins way after the X series ended, about 400 years or so...poor guy lol. We see that Zero is no longer bulky armored correct? Sometime between the end of the X series and the 400 years thing Zero must have gone through some sort of upgrade, or in this case, a slimmer and more human look. So they transferred all of his memories and such to that new style body.

We find out in one of the later Zero games that Omega stole Zeros original new body and Zero got a replica. Later on he was heavily damaged and needed to "Sleep" during that time there was an attack and he was defenseless since he was unconscious and that added to his damage and then some. Not only was he hurt from the attack by mavericks (had to of been) the lab he was resting in was laid to ruin and so was he. A cyber elf found him centuries later where we find him in Zero 1 :D. That cyber elf decided to fuse with him in order to repair him.

Ok so now I'm skipping ahead to between end of Zero and beginning of ZX. People get confused about the whole Ciel discovering the Weil remains and Serpent stealing them and Albert creating model W thing. It isn't that difficult to sort this out. Weil can't die correct? Yes, technically he can't, he is immobile and also can't speak or pretty much anything so he is believed to be dead.

Truth is Weil was still live and well (lol sorta) even after the final battle with Zero. Ciel DID discover Weils' remains and saw that there was still living tissue. The living tissue was the Biometal that Albert secretly left behind for his future plans for world domination. Albert apparently was the very first to create such a thing and he wanted Weils' powers too but at a greater scale, and that is why he decided not to act THEN but instead waited for years.(since reploids do in fact have blood/DNA despite Zero being ripped apart at the beginning of Zero 1...he had an excuse for living...he had the cyber elf)

She gathered the living tissue and studied it along with her colleagues including Serpent. As she figured it out she used it on all of the legendary heros of that time period for preservation. Shortly after doing so Serpent went nuts and stole the Model W Biometal. Albert and Serpent knew each other apparently but only after he'd taken off with the Model W. As if being corrupted by an evil entity known as Weil wasn't bad enough Albert began putting thoughts into his head to further ensure his great plan. Serpent went along his merry way and Albert found the remains area or as we call it "Area N" You know where I'm heading with this don't you? Albert found Omegas remains and instead of just creating a biometal, he completely revived him all together because there was enough of Omegas body left over for it. Truly there IS no actual purpose for Omega to be around but I think that Alberts' thought was maybe the chosen one for Zero would stumble across here and get murdered. Truthfully Omega had already served his purpose long ago and was pretty much just an extra...useful, but obsolete.

That is what all happened in that time period between Zero and ZX.