I set Headmasters in an alternate timeline, actually. TECHNICALLY there'd be a timeline BEFORE T2006 or Fallen Angel where Cyclonus and Scourge were under Scorponok's command, however we have no way to know WHEN they first arrived. Hence my only listing that in my timeline B, as the Headmasters stories we know occur AFTER Galvatron's arrival, therefore they could have arrived at any time before then (Creating a timeline into which we have no idea which stories would fit, all of the ones pre-T2006, none of them, etc) or after then (immediately before Headmasters or between T2006 and Headmasters). For neatness' sake, and based on the fact that both they and Galvatron seemed to be from similar enough timelines, I just lumped them together.
My timelines are getting a LOT more complex right now, and I'm looking at, once I have continuity established for all the issues, THEN making an interactive timeline where you can choose which variables to take into account.
*edit*
Okay, Time Wars just gave me an idea of where this continuity can fit in.
Galvatron initially arrived, and carried out his plans, but in THIS continuity, the events of Dry Run do not take place. With no Cyclonus and Scourge, there is insufficient damage to the fabric of spacetime to open the rift. The battle of Time Wars takes place, with Megatron and Galvatron against the Wreckers and Mayhems. Now, after the battle the two of them rest, and wait. When they are recovered they pursue the autobots and decepticons, however none of the future transformers arrive to confront them, and they eventually triumph against Optimus Prime and the others.
In this future, they take command of the Decepticons, and eventually events analogous to the movie occur, Straxatron becoming Galvatron and heading back in time to carry out what he previously saw Galvatron do.
This is where things mess up. The timeline he returns to, Cyclonus and Scourge arrive in from the future. They interfere with the course of events causing the accelerated growth of the rift from of Time Wars. This leads to the future Autobots and Decepticons heading back in time. Things are exacerbated when this new Galvatron attempts to use his memory of what he experienced as Megatron in order to give them an advantage, pursuing the Wreckers and Mayhems. This leads to the conflict with the future transformers, and the results we've seen of Time Wars.
An example of this continuity can be found
HERE
And what's even better?
Two pages, a load of timelines, and FINALLY I've got an answer on where those damn micromaster stories fit in.
Here's a fully annotated version of this one, for context.
