Okay I'm reasonably sure that no mention of him was made in the IDW prequels to the first movie and the Reign of Starscream, SO Megatron was working for The Fallen all along (As per the IDW Comics that chronicle the beginning of tension on Cybertron - I forget the name right now). He flies back to the NEmesis to find the Fallen tied into his throne (life support?). Was the Fallen there all along? He wasn't mentioned (AFAIK) in the prequels/set up fiction to the previous movie, and leaving out something like the all powerful semi God of a bot you're working for is along for the ride seems like something big to leave out... I suppose what I'm asking is, is it one of those things like the Matrix in G1 suddenly appearing in TFTM that we're just asked to run with and presume he was there all along, or did he come to be in the nemesis at some later point after the previous movie's prequel material.