If I took over the TF movie franchise, this is probably what I'd aim for (which I posted previously, but have slightly altered/cleaned up here):
TRANSFORMERS 2: THE CHAOS-BRINGER
Megatron being fused to the Allspark has caused his intellect to be joined with the Allspark's creator - Unicron, who devised it not to create life, but to "infect" worlds and consume their energy in order to build up the power necessary for him to regain corporeal form. Wishing to usurp Unicron's might for his own, Megatron consents to become his minion - at which point Unicron channels the power of a black hole into Megatron's lifeless husk (mirroring G1 Megatron's ability to channel black holes to draw power for his fusion cannon), causing to burn it right through the ocean floor and Earth's crust, into the planet's volcanic innards to galvanize his new form, hence his new moniker...Galvatron.
Following this, Starscream comes back to Earth with his fellow Seekers, Thundercracker and Skywarp, and their communications expert Soundwave, to retrieve the remains of the other dead Decepticons (still intact at the bottom of the Laurentian Abyss due to their Energon reserves intensifying from the pressure - and from the intense heat of Unicron's remote 'Powerlink' to Megatron's corpse - to create counteractive 'fields') to construct their own bio-mechanical abomination - Bruticus, a Frankenstein pastiche now under Starscream's control (shades of "Starscream's Brigade") which succeeds in killing Ironhide and horribly damaging Bumblebee in its initial skirmish with the four remaining Autobots. Lennox, Epps, Glen and Maggie are now in charge of a new initiative begun by Def. Sec. Keller - a sort of RAAT/EDC-type organization created for the express purpose of being ready for more trouble from Decepticons - which mobilizes to track them down with the aid of the surviving Autobots.
Meanwhile, Sam and Mikaela's relationship hits the skids when Sam begins having nightmarish visions - later attributed to his exposure to the Allspark's energies when he offed Megatron - of what appears to be Earth's destruction, and they aren't too dissimilar from Optimus' holographic chronicle of Cybertron's ruin. Bumblebee's near-death doesn't help matters, but Ratchet is able to reconstruct Bumblebee to assume a more powerful car form - which leads to the scanning of a gold-colored street racer with a yellow-on-red flame paint job on the hood; Lennox and Epps take to calling Bumblebee's new incarnation "Goldenrod" (in a knowing SW reference to the Han-Threepio relationship; it also homages G1 Bumblebee's eventual rebuilding into Goldbug, and accommodates Hasbro's current inability to re-use the name "Hot Rod").
Amid all this Optimus' closing transmission from the first film results in a grand total of TWO Autobots showing up on Earth to provide backup, comprised of Ironhide's protege Arcee and Starscream's old partner Jetfire. No one thinks much of Arcee until she pretty much becomes a veritable one-bot army in the climactic battle in Washington, D.C. against Bruticus, while Jetfire and Starscream engage themselves in a furious aerial duel as the Seekers start obliterating the remaining Autobots and Lennox's forces. Neither Autobot force gains any real ground - Optimus, Arcee and Goldenrod level blows to Bruticus that do little more than slow him down, and Jetfire's little dance with Starscream is interrupted by the newly-reborn Galvatron, who having emerged from the ocean Gojira-style (fragging a passing ship as he goes) bursts out of the clouds and immolates Starscream for his subversion with one blast (TF:TM '86). With Jetfire sufficiently weakened as to be less than a threat to him, Galvatron tosses him aside and proceeds to bend Bruticus to his will, forcing the other Decepticons to align themselves with him and his new 'recruits' from the ranks of machines given life by the Allspark in the climax of the first film - Cyclonus and Scourge.
The Autobots' last remaining gambit to repel Galvatron's army degenerates into a two-fold sacrifice play: Optimus launches himself at Bruticus and merges his own spark to Bruticus' multiple unstable power sources, ripping himself to pieces and stopping Bruticus in his tracks, but not killing the monster; likewise, as Galvatron prepares to open fire on Optimus to cut off the overload, Ratchet hurls himself into the path of Galvatron's cannon and is obliterated (recalling Ratchet's sacrifice, multiple times, to thwart Megatron in the Marvel comics).
With their leader and their medic now dead, Sam having alienated everyone he loves with his apparent 'delusions', Washington, D.C. now totally destroyed, and Galvatron and his new army on the loose, the three surviving Autobots and their human charge are on the run from an angry humankind that no longer wants their war on our world, as well as a much more powerful and numerous Decepticon detachment bent on a new and more sinister purpose...
TRANSFORMERS 3: END OF THE ROAD
Under Galvatron's direction, the Decepticons have been laying waste to major cities in a bid to draw out the three remaining Autobots. Galvatron leverages humankind's fate in an attempt to co-erce Lennox's team into capturing (and preferably destroying) Goldenrod, Arcee, and Jetfire - but demands that Sam be brought in alive at all costs, having determined that he now shares a psionic link to the young man as the result of their shared exposure to the Allspark. Galvatron has realized that any human that could contain even a fragment of the Allspark's power could augment his own considerably, and plans to "upgrade" Sam into a bio-mechanical minion - a "Minicon", his underlings playfully describe it - who can interface with and bolster Galvatron's internal systems enough to strike at Unicron when the Chaos-Bringer least expects it. It is during an early surprise attack on the Autobots by Soundwave that Sam is captured and the Autobots are finally detained by Lennox's crew, who seem to take their sweet time towards exterminating them (reluctant to do so given their past alliance).
Realizing from news footage of the battle that Sam's hallucinations may be tantamount to something far greater, Mikaela risks her own life to break into the Arctic encampment where the Autobots are awaiting termination, impersonating an officer and liberating the captured Autobots - with a little help from Maggie and Glen, who have been monitoring the entire exercise - and Goldenrod resolves to infiltrate Fortress Maximus, Galvatron's stronghold atop Devil's Tower (a Spielberg nod there, as well as an ode to the 'Con's mountaintop fortress in the old Marvel comics) to save his friend. In the escape, Cyclonus engages Jetfire and the two plummet into the glacial shelf, ending in a massive explosion caused by Jetfire detonating his munitions store (a la Jetfire's fate in the Dreamwave books), leaving only the smoldering skull of Cyclonus tumbling back to the earth (a combined nod both to Jetfire/Skyfire's animated origins, and to Cyclonus' fate in "Time Wars").
In a parallel to the first film, four more protoforms crash to the Earth, alarming Galvatron, who's already started subjecting Sam to the painful process of bio-conversion. These four are Autobots, of course - Grimlock, Magnus, Springer, and Swoop, members of a special Autobot detachment that was sent across the galaxy to track down Megatron's most dangerous agents. To destroy the new Autobots, Galvatron decides to make an example of Lennox and his men for their "failure" by subjecting them to one of his other "experiments" - an electrochemical airborne virus created from Starscream's salvaged spark (echoing both the creation of BW Rampage and even hinting at the whole 'Starscream's ghost' bit and the Hate Plague from "The Return of Optimus Prime"), which mutates the unit into living batteries of hatred so powerful they cause their vehicles to assume beast-like exo-skeletal forms that put Scorponok to shame - thus enabling Galvatron to almost replicate the same creation process that the Allspark was capable of, and compelling him to work even more fiercely to complete Sam's "transformation".
Meanwhile, the Autobot 'Wreckers' - having chosen their alt-modes of an armored car (Grimlock), a car-carrier (Magnus), an SUV (Springer), and a helicopter (Swoop), respectively - meet up with Goldenrod and Arcee in a feverish chase/battle sequence in the desert that takes care of Soundwave and Scourge. Under attack by the hate-infested biomechs, the Autobots and Sec. Kelley aren't left with much more choice but to put protocol aside and make their final stand at Devil's Tower, where Bruticus is waiting. Magnus reveals a surprise tactic - merging with his carrier trailer to form a power-armored robot identity, Ultramagnus - which proceeds to tear into Bruticus while Grimlock and Swoop carve up Thundercracker and Skywarp, and while Springer, Arcee, Goldenrod and Mikaela sneak into the tower and finally do away with Cyclonus and rescue Sam.
Springer and Arcee are separated from Goldenrod and Mikaela when the former pair are forced to lure an ARMY of Scorponok clones out into the battlefield in an effort to destroy them in a makeshift demo-derby, while Goldenrod and Mikaela confront the horror of what is left of Sam - a humanoid hulk of metal which Galvatron has already attuned to his own Allspark interface, in the midst of brainwashing him. A duel begins between Autobot and Decepticon, culminating in Goldenrod being crippled by a devastating blow and leaving Mikaela open prey for Galvatron's burning fusion cannon. This act snaps Sam out of his agonized stupor and, shaking away Galvatron's incomplete effort to reprogram him, interfaces his arm-mounted Powerlink pick into Goldenrod's spark chamber, channeling his absorbed Allspark energies to initiate one last reformatting sequence for his Autobot friend; between the two of them, a familiar voice from beyond echoes - "Rise...RODIMUS PRIME."
Armed to the teeth and packing the power of both the Allspark and the increase from being "binary-bonded" to Sam, Rodimus Prime finally, literally blasts Galvatron into ashes, deactivating what's left of the biomech army and the Scorpo-swarm. Knowing Earth will never be safe as long as a single Transformer remains on it - himself now included - Sam bids Mikaela an emotional goodbye, taking on the new designation "Spike" (in reference to his Robocop-like interface pick) and, aboard the reconditioned Fortress Maximus, heads for the moon with the other Autobots to watch over Earth from a relative distance.