One of the problems I've had with the comic is the timing of the various storylines. This particular storyline was supposed to start much earlier in the overall timeline, back in the middle of the second game storyline, in fact. As has been mentioned, Mynd was supposed to attack the Megaman Universe before Mega Man, Bass, and X returned the present, so it would be easier to take over. If I had planned things better, I probably should've switched back and forth between the two storylines, but I got so hung up on the Megaman 2 storyline, I completely forgot about this plot thread until this point, requiring the awkward transition panel seen above.
As it is, this storyline is supposed to take place shortly after we saw Mynd, as the mysterious shadowy villain, turn off his monitor and was left in the dark. Though, I suppose there has to at least have been enough time for his eyes to adjust to the darkness.