That Zero sure is comfortable in Cyberspace, eh? Yeah, and with that E-Reader card, the enemies of Megaman Zero 3 become Virii from the Megaman Battle Network series. And then suddenly the Z-Saber chip changes into the MMZ Zero... ...coincidence? No. I believe that Copy Zero is Zero.EXE, who mysteriously vanishes after his initial appearance. The Internet has warped reality in very strange ways in the MMBN series; I'm sure crossing over between MMBN and MMZ is no more of a stretch than MMBN and MMSF.
But why have a "weaker" Zero fight?
That's because this is all a convoluted plot on the part of none other than the perverted Megaman X to off his long-time rival-in-flirting! X knows that Zero's own worst enemy is himself, so he waited for two rounds of long-haired, blonde, and ambiguous sword wielders (Elpizo and Omega) to get the better of this Copy Zero and destroy X's main body! In this way, X no longer has to fight! Weil was eventually the one to destroy Copy Zero...
But no, it doesn't stop there! X also knows that Ciel would inevitably try to find a way to revive him and Zero. Change a few of Ciel's data files here and there, and suddenly, X can be revived in the form of a Biometal, allowing him to choose the girl of his choice, rather than limiting him to a few Navigators that are insane in the membrane!
Lo and behold, X finds Aile through the news of the Maverick attacks! Notice how much she likes "Rocking On" (yes, he's that dastardly). And then, when Zero (as Model Z) tries to muscle in on his find, X takes advantage of Zero's naivete, something X was once criticized for, and tricks Zero into "sacrificing himself" (see: kicking out the roommate)!
So centuries' worth of planning, just to find the finest girl ever! Who would be so genius, so much of a devious mastermind, to plot such a venture? Why does a reploid care about the physical attributes of a human girl he doesn't even know?
Well, if you believe what you've heard about him, Dr. Light is more than he seems.