That was thoroughly enjoyable.
You set up a very interesting plot here, and I'm looking forward to seeing how you unfold it before us. I'm also counting on you to come through with your allusion in the author's comments to bring Protoman into play (everybody's favorite wrongly accused hero). Question: Was Megaman suffering from a breakdown and Zero from a virus, or what? Be sure to include an explanation in the episode/s to come. Also, you don't have to lay it all out on a silver platter all at once, give us little pieces and clues throughout that will finally add up to the big explanation at the end. Get some more practice in with you animation skills so you can do all the things you clearly want to, and the fights will be absolutely epic (mind you, I found them quite satisfactory as is). Try to fix the text so that it stands out fromt he background. Maybe you could leave a blank space at the bottom that you can just fill with text as it's spoken, as you also had a bit of unused space at the bottom of your screen. Good job, and keep it up with the next one.