It's a blissful time for the now firmly established Galactic Republic. In one of the few periods during the Star Wars Expanded Universe, the government hasn't been at war. In fact it's been three years since the last major conflict. There is peace and prosperity, something the former Rebel Alliance fought fiercely and died for. They are now the supreme power in the galaxy both politically and militarily. The Republic has even managed to make a lasting peace with the remaining Imperial Remnant. All sectors are quiet.
You know it won't last!
The all-powerful God of Chaos in the Transformers Universe has regrouped after his last defeat and is now looking to branch out into new territory away from the prying eyes and consciousness of his "brother" Primus (the planet Cybertron). On the fringes of Galactic Republic space, he begins his encroachment. Slowly but surely, attacking and consuming planets with very little life, gaining strength with each successive consumption.
But, while he's doing this, he needs an army to run interference until he gains sufficient strength to take on the Republic war machine directly. It's an army the GR will find all too familiar to their chagrin.
The Yuuzhan Vong
I know what you're saying. The YV grow their tech organically. A purely mechanical being like Unicron would be an abomination in their eyes. Why would they agree to help him? The answer? They haven't.
Part of Unicron's power is to subjugate his "allies." Apparently, this power can expand to a whole race. Tired of the constant failures of his previous allies, the Decepticons, the Chaos God decided it was time for new blood. The YV are the perfect distraction while he feeds and gains strength. They're a terrifying enemy of religious zealots that almost destroyed the Republic themselves many years ago.
Autobots to the Rescue
Even in the far reaches of the galaxy, Primus can sense his brothers return and he alerts his greatest creations, the heroic robotic warriors, the Autobots. Their leader, Optimus Prime, takes a small squadron of his most trusted warriors into GR space.
They don't find Unicron initially, but they do find the YV up to their usual antics of terra-forming conquered planets. Acting to save the inhabitants of one such world, they are mistakenly attacked by the GR military. Taking heavy damage, Optimus refuses to have the Autobots fight back. Their mission seems doomed to failure until their true intentions are sensed by another group that has accompanied the military to repel the YV.
The New Jedi Order
Led by Grandmaster Luke Skywalker, the Jedi Order is powerful and plentiful once again. Grandmaster Skywalker and many of his knights remember all too well the damage the YV caused before. In fact, it was their machinations that were the early catalyst in the downfall of his nephew, Jacen Solo.
Recognizing the Autobots are there to help, Grandmaster Skywalker brokers an alliance with the giant machines. Together, the GR and Autobots develop a plan of attack.
Back on Coruscant, it's decided that the main Autobot force along with a large group of Jedi warriors led by Jaina Solo, Han and Leia Solo's daughter and Luke's niece, will assist the GR military in repelling the fiercer than ever Yuuzhan Vong.
Optimus and his chief lieutenant, Bumblebee, stay behind with the Jedi High Council to formulate a strategy for finding and destroying Unicron. Well, they don't have far to look. Soon after the main Jedi/Autobot force leaves Coruscant, Unicorn, in his planetary form, invades Coruscant space.
While formidable, the planetary defenses are no match for a god. As Unicron prepares to destroy Coruscant, Optimus, Bumblebee, and the Council launch a desperate counterattack. Providing a distraction, the Autobots play decoy while the Millennium Falcon lands on Unicron's planetary surface. Through the Force, the Council and Leia (also a Jedi Knight by this time) probe the god to find weaknesses. Monitoring the action in space, Han sees the Autobots' small spacecraft severely damaged by Unicron.
Coming up with a suicidal plan, the Jedi depart the Falcon to the surface. Han takes off in the Falcon to aid Prime and Bumblebee when the unthinkable happens. Unicron transforms into giant robot mode and catches the Falcon mid-flight. Then with a simple crunch of his robotic teeth, Captain Han Solo and the Millennium Falcon are no more. His final moments of anguish are felt through the Force, particularly by his wife and brother-in-law.
With no time for despair the Jedi don't have much time to act. The ten Jedi Masters and Leia join hands and concentrate. With the Force, they continue to push outward against Unicron's surface each building on each other's strength. They keep pushing and pushing. Cosmic storms and whirlwinds begin to form around the giant as pressure continues to build. And, then, finally, the Force finds the evil god's breaking point. In an explosion whose ripples hammer the nearby Coruscant, Unicron's body explodes in a fiery ball of flame. The remnants of the Autobots' craft is destroyed. But, they are metal constructs who can survive the rigors of space for undisclosed periods of time. The Jedi, being flesh and blood, cannot.
Grandmaster Skywalker, Leia Solo, and the Jedi Masters of the High Council all perish in space when Unicron is destroyed.
Helping to rebuild Coruscant after the YV are driven away, the surviving Autobots are ready to depart for points unknown. Before leaving, Optimus Prime entrusts a device that can alert the Autobots should Unicron show himself again to new Jedi Grandmaster, Jaina Solo. Jaina watches the Autobot ship leave Coruscant space, and, then turns to enter the rebuilt Jedi Temple to convene a meeting with the new High Council. As she passes through the halls of the great Temple, the ghost of Luke Skywalker appears smiling in approval.