OK, I just read this through and I am going to do a proper review now. GOOD LORD! I thought MY Megatron was evil! But you've got here a Voldemort/Megatron hybrid that is freakishly frightening. And the whole Black Arachnia/Bellatrix thing (way to rile Starscream by the way) is creepy.
I personally avoided Black Arachnia since she was from Beast Wars/Machines rather than G1.
Sure I've got a lot of people scheduled to die in my fic but nothing like this! And the bots. The only Autobots we have in common are Prime, Bumblebee, Ratchet, Ironhide, and Jetfire, all other Autobots completely different.
Its the Decepticons we have more in common: Megatron, Starscream, Soundwave, Thundercracker, Astrotrain, Scorponok... OK maybe not. (damn, I'm spoiling myself). Maybe I just have a plain larger cast of Transformers.
Lets see, whereas I ignore the epilogue, yours is epilogue compliant only you've crushed JKR's happy go lucky ending. Not that I'm complaining about that but you did it in such a brutal angst ridden way. You killed Sam and Mikaela off but introduced Daniel (whom if I remember right is from the post movie era when Rodimus was Prime) but then its probably for TF fan recognition anyway. You've given several off-handed remarks of the "Chaos Bringer" here whereas I only mention Unicron in passing.
Nope, mine is nowhere near as dark as yours. In my universe Elita-One is still alive, the DH epilogue never happened, Harry doesn't smoke, and Starscream isn't as cowardly though he's every bit as treacherous. I think the biggest differences is that mine is just plain slower pace.
So the minister is on the Decepticons side? How strange... 
, tricky situaion for Daniel...whatever he says he's going to hurt a girl he cares for...
Adn good luck writing this.