I imagine the relevance of this story is easily missed.
So, let us travel back to 2010, and the final page from Monkey Squad One #6:
So, basically, the scene in MS1 Annual #2 is an extension of this scene, but we finally get to meet Professor Metropolis and see him in action. Plus we kind of see why Malcolm Bliss was confused & thought Dr. Metropolis was Professor Metropolis in MS1 #10.
Look, if I cared whether or not it was confusing, I wouldn't have done a parallel dimension/time-travel story!
APPLES & ORIGINS CONTINUES!