why does megaman and protoman use a program advance together to delete only one navi? why not both of them then?

They probably meant to aim one at each, but they didn\'t exactly have time to discuss who was going to aim at who, so they just picked one and fired. Or not.

Now for this public service announcment: Remember kids, don\'t think to hard about anime. Your head will explode before you get close to figuring something out.

and Maybe they realized that a single one wouldn\'t have been enough

i think megaman X .exe is right mayybe it would not do a lot