Thank goodness it wasn't really Protoman behind these actions against robot and mankind. See, after the rescue of Kalinka from his fortress, Dr. Wily disowned Protoman and hatched up a scheme to frame him for all of Dr. Wily's evil doings. But now that the REAL Protoman has destroyed the disguise of Darkman v4, Dr. Wily's original plan is ruined.
But even though Protoman's name has been cleared, Dr. Light is still a prisoner in Wily's new fortress. Although Protoman has helped Megaman at his most vulnerable, all he could offer him at this point was the location of Dr. Wily's fortress. And as an added help, Beat is able to give him an easier idea as to where to head at from a distance. It's all up to you Megaman, save Dr. Light and bring Dr. Wily to his knees once again!
