There seems to be two (but perhaps even three) distinct forces at work in ReGen1 -- Primus, Unicron and the Dark/Anti-Matrix Energy Monster.

Primus did genuinely take over Grimlock's body back in Issue #94, and then took Hot Rod through the multiverse to give him information, as well as the Matrix, to transform him into Rodimus Prime in #0. It's been said in the series that 'energy cannot be destroyed', so perhaps Primus survived his 'death' in Issue #75 of the original Marvel run and is now trying to get his 'plan' back on track. Why I believe this to actually be Primus (and not the energy monster tricking Rodimus) is because of the distinct change in speech pattern.

I believe that plan to be the minds of the Underbase becoming something of a replacement for Primus himself. The (now) five minds in the Underbase become The Guiding Hand of the IDW universe.

The Dark/Anti-Matrix Energy Monster Thing wants to expand its reach into the entire multiverse, instead of just being contained in the Marvel universe. Sounds similar to what D-Void wanted/wants from what I've read on the TFWiki. Perhaps using Spike as a host, it can traverse the 'crack' in space and time and thus spread.

Ultimately, Rodimus will make some kind of sacrifice or drastic decision that leads to the Energy Monster not succeeding, this time. But he can't destroy the monster outright because 'energy can't be destroyed' blah blah blah. The Marvel Universe becomes the Dead Universe.

Unicron is having a last hurrah, and has taken over Galvatron's body. "One will become all" was a line in a previous Issue (just after the head in the Primus chamber killed all the Unicron Cultists) with emphasis on the 'one', perhaps. Could this not just be the Energy Monster as well? Maybe, yes, but we had Unicron threatening Optimus Prime right the way back at the start of the series and we've not seen hide nor hair of him since.