Unicron is the one behind everything--the war, the decay of Cybertron--all orchestrated by him manipulating things from afar, and when everyone finally learns this, its enough for all sides and factions to put their war on hold and focus on fighting the real enemy for their mutual survival. Even Starscream becomes a voice of reason when he realizes Unicron the puppet master trying to ruin the future for everyone.
The Maximals and Preds are the descendants of a future where the Allspark never makes it back to Cybertron, and they are hounded by Galvatron and Nemesis Prime on Unicron orders. BW Megs goes back in time with the Golden Disk intending on making sure Decepticon Megs changes the past by getting the Allspark and never becoming Galvatron. Galvatron and Nemesis Prime themselves also want to change their fate by manipulating the timeline, but selfishly only want to save their timeline and don't care about anyone else's. So I guess we're using Multiverse Theory when it comes to time travel.
BW Megs acts like a fanboy around Deception Megs, and while its fine at first, it does go a little too far in my opinion. Though there is a line he says during a battle with Primal then kinda implies that he's just bidding his time, willing to play the role of a servant until the opportune moment to seize power for himself, but the line is ambiguous enough that that could just be me reading into it too much.
Dinobot of course makes his brave last stand, managing to defeat both Soundwave and Deception Megs in battle to get the Matrix of Leadership before being mortally wounded by BW Megs, but he does hold out long enough to give it back to Prime. He dies with honor, but it doesn't hold a candle to his death scene in the original show, since we barely got to know him or explore his relationship with other characters.
Blackarachnia and Starscream team up, and you know how that goes. Both of them backstab each other constantly until the realize they got bigger problems.
Silverbolt isn't in this, but he is kinda alluded to when in one scene Blackarachnia has an illusion thrust upon her and she sees a silver wolf beast hunting her that scares her. So don't get your hopes up for that romance. Speaking of, here Blackarachnia flirts with Airazor and comments that Arcee is the "cute pink one" so I guess this version of the character only likes female 'bots. (And yes, there's already fanfiction and fan art for Blackarachnia x Airazor because the internet is fast and thirsty as fuck.

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Optimus finally gets his shit together more or less and gets both the Matrix and the Allspark back and saves Cybertron. The Preds and Maximals hitch a ride onto their timeline since there's was shit and they are all that is left. They all agree that Cybertron is big enough for everyone... for now, until the threat of Unicron is dealt with. Both Megatrons are pragmatic enough to put the war on pause, but aren't giving it up entirely.
Unicron saves Galvatron and Nemesis Prime from death, and while angry at their attempts to break free of their servitude and failure to complete their orders, notes that their use of the Dead Universe to time travel gives him an idea, and it ends with Unicron about to make his move.