A simple copy/paste. Turn off annotations in the original video to see a little bit of the Japanese logo. In addition,Craig brought this to my attention:
"The creator of the video is a friend of mine, and if I know him, he is good at hacking and video editing. Now from what I've seen here is called Keyframing(something to put an image over a video), he used Sony Vegas along with probably good old paint to edit this, along with playing Ryuusei no Rockman 3 on an emulator.
Notice the intro's flaw in not being copyrighted to Nintendo and the intro "fades slowly" and seems just too high quality for an intro. He must have moved and replaced(after editing an image of the black ace title)with the english title using keyframing or maybe a gif animator. And he recorded the emulator playing the rom, taking the video and replacing it as audio under his new title, something quite simple to do.
I noticed their is no such thing as Plasma Gun1, he keyframed a new battle card bar under over the video in just the right placement, that new image was edited from probably picturing the bar and edited with sprite textures of the english text from sprites of sprites inc I'm guessing. Also it would be really hard for him to do the story thats why it skipped to a battle he just put in there, the deletion time status is also wrong as you can see it seems badly put in if it were in the game."
Many thanks to Craig and Kyouya Garyuu.