Every Cybertronian was created by a mystical object called the Allspark. Wherever the Allspark is, it creates life, and also a source of energy called energon. The Cybertronians lived in peace for a time, and built cities and civilizations. But soon a group of Autobots rebelled against the leaders of Cybertron. They soon coined themselves the name, Decepticon for their deceptive ways. They formed a council of leaders and began their war with the Autobots. Civil War raged across the planet for centuries, and the cube somehow disappeared off the face of the planet. Both the Autobots and Decepticons didn't realize at the time that the cube had left the planet. Soon, as the war raged on and ravaged Cybertron, the energon supply on the planet grew low. Both the Autobots and Decepticons were running dangerously low, and they both new defeat was imminent if new energy wasn't found.
The current leader of the Autobots, Sentinel Prime, began a secret project of a grand spaceship called the Ark. Its purpose was to take a team of Autobots, and go into space, looking for a new energy source. Soon, the Decepticons caught wind of this construction, and began work on a ship of their own, the Nemesis. Its prime purpose was to destroy the Ark, and go in search of more energy to fuel their armies.
Soon, the construction on both ships was finished, and they both started to prepare for the voyage. Sentinel Prime appointed Ultra Magnus as the head of security. His job was to recruit Autobots, and guard the Ark until it’s departure. The Decepticon leaders knew that if they were to find a source of energy to supply their army, they would need to find a destination. They instructed a former scientist and explorer, Starscream, to find this new planet. So Starscream traveled into the depths of space, in search of a planet wit a sufficient energy source.
A former criminal and Decepticon leader known as Megatron soon became greedy for more power. He wanted to rule the Decepticons by himself, without the Decepticon council. The Decepticon council had been watching Megatron for years, knowing of his plans for treachery. They decided it was coming time to kill him, for fear that he may kill them all. Unfortunately, it was already to late. Megatron ordered his trusted gun toting trigger-happy demolitions expert, Bonecrusher, to blow up the council. He did as instructed, and Megatron became the sole leader of the Decepticons.
As new Leader, Megatron knew it was time to take out the Ark. He had a group of spies infiltrate the Ark, and plant a bomb. Meanwhile in Space, Starscream had been searching for over a decade in search of the perfect planet. Somewhere along the way, he went through a time warp, and entered the Milky Way galaxy. He discovered a planet with a high-energy reading, earth. He radioed back to Cybertron with his discovery, and went to earth to explore for himself.
Back on Cybertron, Sentinel Prime caught wind of the Decepticon craft’s construction, and had a spy, Bumblebee, infiltrate the Nemesis. Unbeknownst to the rest of the crew, Autobot spy Jazz had also infiltrated the Nemesis. (Its our guess he had come across it during one of his missions, and investigated.)
Both spies aboard the ship discovered Megatron’s evil plan and the secret bomb hidden on the Ark. Bumblebee was injured during his mission, and damaged his vocal processors. He quickly fled back to the Ark, to warn his teammates of the danger.
On Earth, (2003) Starscream investigated. He discovered that the dominant creature on the planet, were flesh creatures who use technology to do what they cannot. He took the form of an Earth jet, and went in search of a secluded island, to begin work on a secret lab. Before he left Cybertron, he smuggled six Decepticon mutineers’ sparks off the planet. These Decepticons tried to kill Megatron, and as punishment, they were stipped of their bodies, and their sparks were put into containment (jail). [the six Decepticons are the Combaticons] His plan was to begin a small army to over throw Megatron. He is currently building bodies for the six Decepticons, and building his lab. His plan is to have his lab finished before Megatron gets to earth, so he has a secret base that Megatron is unaware of, to aid his coming rebellion.
On Cybertron, Sentinel told his young friend and first in command, Optimus (not yet Prime) that if anything happens, he will be the new leader of the Autobots. Soon, Bumblebee makes it back to the Ark. He warns Sentinel of the bomb, and they go to find and disarm it.
Megatron and his Decepticons are now ready to depart. He gets his crew onboard the ship, and promotes Shockwave. He makes Shockwave the leader of the Decepticons on Cybertron in his absence, while Megatron leads his men in space. As they load onto the Nemesis, Megatron activates the bomb’s countdown on the Ark.
Back on the Ark, Sentinel and Bumblebee find the bomb. They are unable to disarm it, and Sentinel activates the Ark’s intercom. He informs his men that he is going to die sacrificing himself, and appointing Optimus to leader [Prime]. Sentinel takes the bomb, as it goes off. Somehow, a rift in time occurs, and Bumblebee and the Matrix are sent to earth. Because the official transference of leadership never occurred, the Matrix was with Sentinel as he died. The Matrix was blown into space, and went through a time rift, sending it into the 1880’s. It crash landed on earth, and has been there since. Bumblebee also got sent to earth [Year 2007] somehow.
As Optimus’s first order as the new Prime, he prepares the Ark for its lift off into space. As it begins to take off, the Nemesis also lifts off. In an attempt to make sure the bomb did its job, Megatron takes the Nemesis to the Ark’s launch pad. There, he discovers the bomb didn’t destroy the Ark, and opens fire on the ship. The Ark returns fire, and the two engage in a standoff. Megatron moves the Nemesis next to the Ark, and begins to board the Ark.
Now, Megatron and his team of Decepticons are fighting with Autobot soldiers led by Optimus in the hallway connecting the two ships. [Think beginning of Star Wars Episode IV] The two ships are slowly making their way off Cybertron in the midst of the conflict. Jazz is also trying to get off the Nemesis, and is in the hallway trying to get back on the Ark, lest he is left behind enemy lines. I excluded some details that pertain to character’s plotlines, but are irrelevant to the overall plot.
That’s basically the sum up of everything so far.