The storyline I know seems to be a combination of the armada/energon cartoon and the comic to which you prefer.
Basically, Unicron destroys everything. Primus hides in a giant body of mass that is later formed into Cybertron by the Quintessons. THe QUintessons essentially turn the planet into a giant factory, creating slave bots and gladiator bots. Primus awakes, and begins implanting sparks into these machines forming them into what later became known as Autobots and Decepticons. The Quintessons try to destroy Primus and his "children" so Primus joins himself to the Quintesson creation matrix to form Vector Sigma. Under his guide, A-3 (aka Alpha Trion) defeats the Quintessons.
Then the various struggles between the decepticons and the autobots ensue. Maximo destroys Primon (Primus' physical form and guardian of sorts, taht originally contained the Matrix) and combines himself with the matrix, thus transforming himself into Liege Maximo. The autobots get pissed. War ensues. The autbots become guardians of the matrix. Primus uses "the Guardians" (the converted Quintesson "Dark Guardians" used to defeat the Quintessons) to stop the war between the two factions. Peace takes hold of the planet, and the various religious sects form, one of which believes that the Matrix is a weapon to be used against Unicron.
Peace breaks down, more wars ensue, Cybertron's resources are depleted. Optimus leaves to find more resources. Megatron pursues. Fast forward a bit and you end up in 1984 on planet Earth.
That's about what I remember.
