Against my better judgement... some ideas I've been toying with in my own head. If KingSwoop doesn't like them then nuts to him...
Start with a huge battle on Cybertron. Sentinel Prime and Megatron are fighting on an elevated platform akin to Optimus and Megs fighting on the damn.
I'd crib dialogue from their fight in Megatron: Origins because it's that damn good IMO.
Eventually Megs and Sentinel each fall through the structure they were fighting on and Megs kills Sentinel. He goes to rip the Matrix from his chest but ala TFO it disintegrates if claimed by the unworthy.
Megs is enraged. He wanted the Matrix and the power it represents but it's been lost just when he could claim it.
Megs emerges from the wreckage dragging Sentinel's corpse and tosses it into the battlefield. He proclaims he's slain "the last Prime" and willfully destroyed the Matrix to free Cybertron from superstition. The Autobots, shocked and demoralized, retreat and the Decepticons make a push to conquer the planet.
Orion Pax is a dockworker who was drawn to the Decepticon cause for social egalitarianism, against the wishes of his friends Ariel and Dion who think Megatron's been getting too violent to effect any positive change.
Orion doesn't heed their warnings though, and joins the Decepticons. Hell, maybe even have Orion be an old friend of Megatron. One's a miner, one's a dock worker... not inconceivable that they'd meet in organized labour circles early on.
Orion, though, has grown fully disillusioned with Megatron by now. Megs is openly slaughtering entire cities that don't just surrender to the Decepticons, he's torturing POWs, executing the innocent for mere suspicion of being Autobot sympathizers... he's had enough. He tosses his Decepticon badge off and tries to make contact with Ariel and Dion, his two old friends who he knows are safe behind Autobot lines.
Megatron gets wind that his friend had abandoned the cause and tries to chase him down, and he ends up mortally wounding Ariel and Orion, and killing Dion. I'd play it like Megs would try and talk Orion back/Dion and Ariel to his side, but when it doesn't look like they'll listen he loses it and in a fit of rage does the deed(s). Once Megatron realizes he's killed one of his friends and grievously wounded two others he steels himself. If they won't join him they'll perish like the rest of Cybertron who refuses to join him. He goes to kill them but Alpha Trion appears and forces Megs into a retreat. He then saves Ariel and Orion.
Orion is rebuilt into Optronix (thanks
@Undead Scottsman!) and Ariel info Elita. Alpha Trion explains that he helps the Autobots when he can but he can only do so much. Still, he tries because he feels responsible.
Optronix asks why. Alpha Trion replies that his real name is Alpha Prime, one of the Thirteen, second oldest only to Prima. He's the only survivor and changed his name so his siblings' legacy could be remembered fully and that Cybetronian society could develop on its own without them looking to him.
He's watched Prima's Matrix get passed from Prime to Prime, but he put too much faith in it. He knew anyone who was accepted by the Matrix would have to be worthy and thought that was enough. Only too recently has he come to understand that to be worthy isn't enough, one has to prove themselves to be continuously worthy. Too many Primes... Guardian... Nova... Nominus... Sentinel... they may have been worthy once but they let that power lead to complacency and arrogance and now this war is the price.
Optronix says it doesn't matter, Megatron destroyed the Matrix, but Alpha Trion doesn't believe that. It can't be destroyed, it's an aspect of Primus himself.
If this war is to end a worthy Prime- one who will be an example of how Cybertron can better itself- will need to arise to oppose Megatron's seemingly unstoppable march. They need to find it first. Alpha Trion sends Optronix and Ariel to Vector Sigma, the supercomputer at Cyberyron's core. If the Matrix is anywhere it's there. He gives them the key to Vector Sigma.
Along the way they run into an Autobot strike team of Ironhide, Prowl, Jazz, Bumblebee, and Ratchet as the medic. Ironhide's ready to take them prisoner as he recognizes Optronix as Orion Pax, Megs' former friend and Decepticon, but Elita produces her Autobot badge and Optronix produces the Key to Vector Sigma.
Optronix says Megatron is on the wrong path but if they can find the Matrix and someone truly worthy to wield it then maybe, just maybe, this war can end.
The Autobot team takes Optronix and Elita in and they begin their quest deep into the core of Cybertron. Along the way they find organic rock and dirt packed in alongside metal and circuitry, suggesting an organic component to Cybertron but we don't linger on it.
Megatron, meanwhile, has found out about this quest. When Alpha Trion stopped him from offing Orion and Ariel he sent Laserbeak to keep tabs on them.
He's leading a team of Decepticons to intercept them. If the core is where the Matrix is then maybe he can still somehow get his hands on it.
As they get to the core they find the key doesn't seem to work, but before they can figure out what to do Megatron shows up with his backup. Optronix tries to reason with his friend, that his path has led to the destruction of Cybertron and that there's no just peace that can grow from his actions. Megatron seems to struggle with this but doubles down.
He angrily beats Optronix and goes to execute Elita, blaming her for "turning" his friend Orion against him but a brutally beaten Optronix takes the blast and seems to die.
Megatron is livid but before he can do anything else the key to Vector Sigma activates and the core glows. Everyone sees the Matrix emerge from the core and Megatron reaches out to take it. He thinks it'll be his but it zooms past him embedding itself in Optronix' prone body. The Matrix revitalizes and reformats him as Optimus Prime.
Optimus leads the Autobots to force Megatron into a retreat and he emerges on the surface. For the Autobots this is a miracle. They thought Megatron destroyed the Matrix. Optimus is able to display, via his ability to command Titans, that he's the real deal. The appearance of a new Prime tallies the Autobots who force the Decepticons into a stalemate.
Because this "Optimus Prime" seemed to appear out of nowhere for the vast majority of 'bots and 'cons alike a rumour begins to circulate that he's not just Sentinel's successor, but the fabled "Arisen," the last of the Thirteen.
This would be played with, with Optimus deeply uncomfortable with the idea but some hints that it
might be true (thanks
@Shadewing!)
That's the setup
I'd establish that after continuous fighting in this stalemate status quo Cybertron and its colonies begin to run low on energy. Yeah, the colonies are a thing and fully involved in the War. Caminus, for example, is Autobot aligned and the "headquarters" of the dominant Cybertronian religion, with the Mistress of the Flame being basically the Cybertronian Pope.
Chaar, meanwhile, is a mining colony that's firmly Decepticon aligned.
Anyway with energy running low and the war dragging into a stalemate Optimus decides to lead an expedition to find more energy. Megatron finds out (Laserbeak is earning is paycheque) and the Nemesis intercepts the Ark. A battle ensures and the Ark is nearly destroyed, but a blind hyperspace jump at the last second saves them.
The Ark jumps into Earth orbit just behind the moon, crashing on the dark side.
Once the Autobots take stock they study Earth and see that while it has energy it has a sentient native species that's fairly advanced. Optimus won't allow it to be harvested but it will make a perfect refuge while they repair the Ark and hopefully get home.
Earthbound Autobots-
Optimus Prime
Bumblebee
Ironhide
Jazz
Prowl
Arcee
Meanwhile, with Optimus and his inner circle gone, the Autobots are pushed back again. Caminus is the lone holdout on the Autobot side, with the Mistress of the Flame's Torchbearer paladins led by Windblade and Star Sabre able to hold the Decepticons back, but just barely. They know, via the sacred Matrix Flame, that wherever Optimus Prime is, he's not dead.
Megatron, meanwhile is relishing in his victory on Cybertron and most of the colony worlds, but it's a hollow victory. Shockwave tells him that energy is mostly depleted and that even with every world under Decepticon command, they won't last. Additionally whispers from Caminus inform Megs that Optimus is alive... somewhere.
Elita is also still on Cybertron, leading an Autobot resistance cell.
Megatron decides that he needs to find Optimus, as well as a new source of energy. He assigns Starscream to lead a team to find them while he shores up Decepticon control on Cybertron and the colonies and continues the war against Autobot-controlled Caminus.
Season one would be about Optimus Prime and his team of Autobots hiding on Earth, trying to secretly gather as much energy as possible to repair the Ark. Eventually they'd find themselves in something of a superhero role fighting human villains for a spell ala Animated, until this catches Starscream's attention.
Late season one would be Optimus Prime and his team on Earth fighting Starscream's team. Who are...
Starscream
Thundercracker
Skywarp
Lugnut
Blitzwing
The Reflectors
Barricade
Starscream will also be planning a coup, thinking that if HE can kill the Prime and harvest Earth's energy he can rally enough 'cons to his side to overthrow Megatron. Lugnut, put on Starscream's team because he's fanatically loyal to Megatron and Megs knows he needs reliable eyes on 'Screamer, will object when Starscream's ambitions become apparent, leading to Starscream killing him and framing the Autobots.
Season one will end with Starscream's forces defeated in their attempt to take Earth, but with Megatron finally clued into where they are.
Season two sees Megatron arrive to personally take command of the Decepticons, in a more traditional Transformers status quo.
I'd also do something where Optimus occasionally has Matrix visions. Sentinel's consciousness would be akin to Avatar Roku from Avatar TLA, someone who both gives some advice and who warns Optimus not to make the mistakes he did that allowed for this war to happen.
Optimus, like Aang, can also confer with his other predecessors from time to time. All but one... the spirit of Nova Prime in the Matrix doesn't speak. He's just a blank void...
While focused on the Earth crews we'd jump around. Some other ideas...
Lockdown, the unaligned Cybertronian bounty hunter who works for the Quintessons, looking for Optimus Prime because the Quints want the Matrix.
The Star Raiders. Thundertron's group of pirates who decide to attack Cybertronian space to plunder what they can, leading to a battle between them and the Autobot paladins defending Caminus.
Eukaris, a beastformer Cybertronian colony divided between Autobot-aligned Maximals led by Apelinq and Decepticon-aligned Predacons led by Gigatron.
Antilla, a mystery. One of the first Autobot colonies that went mysteriously dark. Think the Roanoke.
Will later be reveled to be Unicron's fault somehow.