Finally we're given some idea what's actually happened in the past to disrupt the future. Apparently Dr. Wily is in the process of taking over the world again with eight new robots (nothing new), but this time a black robot (clearly Bass from the future) showed up and destroyed Dr. Light's lab and erased the Mega Man of this time's memory, rendering him inoperable. As to how Bass could do that, keep in mind that Bass is technology from at least a decade in the future, and in the area of robotics, I bet a lot can happen in ten years. He's probably more advanced than anything either Dr. Light or Dr. Wily have seen before. (Though, I bet a closer look at X would make their brains explode.)
My reasoning behind this storyline was simply that if I was Dr. Wily, and suddenly this advanced robot from the future popped out of nowhere and claimed to belong to me, you can sure as hell bet I'd use him to destroy my enemies and help me finally succeed in taking over the world. In fact, if you follow that idea into the present, it explains why we saw a destroyed lab in the background after that temporal shockwave went through.
Also, it can be assumed that between this comic and the previous one, Mega Man probably explained who he was, hence the reason Dr. Light catches himself when talking about his Mega Man in the third panel. I probably just didn't feel like having an entire comic set aside just to explain to Dr. Light who these two new robots were. Sometimes I skip over that stuff and let the reader infer certain details from the conversation.