Personally, I think having Dr. Wily emerge from behind some sort of invisibility cloak is much cooler than simply having the lights come on, which is what happens in the game.
Anyway, with this comic, we start heading into the end of the storyline by reaching back to the beginning and reminding readers that this all began when Bass entered a random portal and apparently screwed something up in the past. Up until now, his presence in the past had been almost completely ignored, but the more mindful readers probably realized it had to come to this eventually.
Although it wasn't explicitly shown, I imagined Bass probably appeared in the past, dazed and confused, and Dr. Wily took advantage of the situation to get him to help take over the world. Dr. Light and Mega Man were completely unprepared for this advanced robot from the future, with his chargeable blaster, faster reflexes, and sassy attitude, and were unable to stop Dr. Wily's plans. This would ultimately lead to the destruction we saw in the present. At least, that's what would've happened had Mega Man and X not then traveled to the past themselves and intervened.
Although, now that I think about it, Bass really isn't a match for this Mega Man, who's also from the present, much less the combined forces of Mega Man and X. A shame Dr. Wily doesn't know that.