Ok, so reading over some TF Wiki stuff, which is just a mish-mash of everything...
Primus and Unicron share a mental link of some kind it seems? Thus why Primus is asleep, so Unicron can't sense him. But when Primus let out his Primal Scream after being shot in the head by some ricochet off Grimlock, Unicron momentarily sensed him, correct?
Something made mention of an Omniversal Matrix, where all the other old Gods are, but Primus isn't allowed to pass there until he defeats Unicron. I don't know what continuity this comes from, but the idea of other Gods is intersting.
My mind says:
Long before he created the Transformers, Primus tried to simply create new Gods, the Lords of Light. Unicron created his armies of Darkness or whatnot. They fought and all perished because they weren't strong enough as you can't create a new God over night.
Unicron and Primus continued to fight before Primus did his old trick of trapping each of them in a planetoid.
Primus then lay his plans for the original 13 Transformers and the creation of the Swarm/Vok to eventually evolve to such a strength and intelligence that they would help him battle Unicron and would be able to defeat him and take both Primus' and Unicron's place as God of the Transformers.
Millenia pass.
When the Vok piggy-backed back to the All Spark/Matrix with Tarantulas' spark, this awoke Primus from his slumber, and whatever level of consiousness this mental connection between Unicron and Primus is on, is where they battled it out.
Unicron mortally wounds Primus, who now lays dying, pleading for his creation to take up arms against his foe, Unicron. The Vok do, evolving to their final stage as a God and get a new snazzy name, lets call him Voxus for the moment, and he kills Unicron on this level of consciousness, as in the real world the Maximals and Predacons battle Unicron's Cybertronian Empire recruits who he has reanimated (Galvatrin style).
Unicron passes into the Void or to the Omniversal Matrix with his other God brethren, and Voxus and Primus have a little chat before Primus too finally joins his brothers and sisters in Valhalla and can be at peace knowing his creations are safe and sound.
Unicron had sunk his horns deep into Cybertron, so the two were joined. An emence power erupts from the centre of Cybertron, reformatting everything and combining the two planetoids into one big thing, like two moons being joined by 2 enormous highways if you will.
TransTech.
The thing practically writes itself.