Think Transformers the movie - Unicron finally comes to Cybertron and so every Cybertronian defends the planet without distinction anymore for whose allegiance is what.
Basically the story is that a United alliance of Cybertronians ( Autos and Decepts) have been teleported back to Cybertron to defend and defeat Unicron. This was done by a Possessed Emirate Xaaron ( the glowing ascending guy) - possessed by Primus himself.
He explains to all his "children that the chaos bringer must be defeated only by joining forces can they succeed and so they did.
Powernaster Prime is struggling to free the goodness in the Matrix ( the one thing which can defeat Unicron) since it has been tainted by Thunderwing's malign influence ( when he has gained control of the artifact - but later on been possessed by the matrix - See Marvel G1 - Matrix Quest). During this time Scorponok is leader of the Earthbound decepticons and has agreed to the alliance and died a hero in Prime's arms while attacking Unicron. Bludgeon takes leadership after....
As the story goes, Prime is able to free the goodness of the matrix but with the cost of sacrificing himself ( Prime's love doing this out of habit :p) which then paves the way for the introduction of Actionmaster Prime but that's a later story. Grimlock gets to be leader ( actionmaster Grimy) as per Prime's last wish relayed to Prowl.
The Marvel run from Matrix Quest onwards to issue 60 in US got me hooked , earlier issues are a bit of hit and miss story wise for me.
In UK G1 comics continued on with Rodimus being leader etc etc, thus have more comic # and also had different storylines, but was effectively tied up to the continuity of US whe Furman took reigns of the comic wrtiting for both. The UK comics has these freebie connect to make a big poster at the middle which you get when you buy religiously the issues - which are hard to come by nowadays WITH them posters ( as per 5FDP):) Hope that helps, other data Im sure Gok can provide