At this point Cybertron's once strong and advance civilization is now in a time of equilibrium. Cybertron is ruled by the High Council who ignore the rule of no underground gladiator battles. One of these might gladiators is one who names himself after one of the thirteen primes, the mighty Megateonus. Later on after being so popular he shortens it to Megatron.
At this time Orion Pax, a data clerk thinking that there is something wrong with Cybertron's Caste System, is assigned to eavesdrop on Megatron's political speeches and report it back to the High Council. When listening to Megatron's speeches Orion is very interested. Confused on how Megatron is thought as an enemy by the High Council he goes to see the last of the living Original 13, Alpha Trion and is anware by the other Cybertronians. Reading the scribe of past, present and future Alpha Trion tells Orion Pax of a great destiny that waits he and Megatron but doesn't know what. Alpha Trion tells Orion Pax to watch his new upstart.
Orion hesitantley joins Megatron's new organization, while in this new organization he enjoys breaking the rules. The two agree that the time has come to form a new Cybertronian government. Megatron thinks this should happen by confrontation, while Orion wants to start this my inspiring others to help change the gaovernment from within. Megatron later adds to his team Soundwave with his army of Minicons and the scientist Shockwave.
When Orion after having a dispute with Megatron, he resigns as being part of Megatron's Organization and soon is viewed as a revolutionary. As Megatron's forces grow more powerful they also begin to grow more deadly by commiting multiple bombings throughout the planet. Later with cooperation with Seeker bodygaurds he kidnaps Sentinel Prime.
One of the Seekers, Starscream is disgusted by the cowardness Sentinel shows during the kidnapping. He tells Megatron that who wants to join him about the Trypticon Station in which Starscream nows about and Megatron does not.
Hoping this won't start a wore Orion Pax and Megatron have a meeting with the High Council. The Council view Megatron as nothing more than a criminal. Megatron during the dispute has named his new organization the Decepticons. When it is Orion's turn to speak he is more noble and compare's this event when the Quintesson's invaded Cybertron along time ago. He proclaims all Cybertronians have fuller potential in life and should be called autonomous robots or Autobots for short. At last one of the Council members Halogen speak and say that Orion and Megatron are right and Cybertron should begin a social rebirth. Halogen declares a new leader is needed in which he tells Orion Pax he will now be called Optimus Prime and his first mission is to retrieve the Matrix of Leadership.
Believing this has been a set up by Orion all along Megatron kills Halogen, but as both sides ready for war Optimus convinces Megatron to stop in which he declines. Instead the two sides retreat and the High Counclil members Contrail and Ratbat align with the Decepticons.
During the war Optimus declares the Autobot capital Iacon, a small part of Cybertron and the Decepticons take most of Cybertrons land and create a capital of thier own called Kraon. An autobot special team called The Wreckers led by Ultra Magnus manage to stand thier own with the Decepticon combiner Devastator. Out of desperation the Autobots launch the sacred AllSpark into space to not let Megatron gain control of Cybertronian life. . During this battle Megatron who tries to get information to the location of the Allspark from Bumblebee fails and destroys his vocal cords.
Megatron creates a new strategy and orders Starscream to take him to Trypticon where there is a stockpile of Dark Energon which is from Unicron himself. Megatron then gets two keys of Justice and Power to open the Plasma Energy Chamber which he plans to dump all the dark energon in to starve the Autobots. The one of the keys were hidden in Sentinel's chest who Megatron killed in combat by ripping him in pieces.
Before Megatron can activate the Chamber, Teletraan- 1 awakens Cybertron's ultimate guardian, Omega Supreme. Transforming from city mode to rocket mode he crushes Megatron and his Decepticon forces. All seems hopeful till Starscream and his Seekers show him and shoot down Omega Supreme in which he lands creating a huge crater. Autobot Medic Ratchet saves Omega Supreme's life but nobody can stop a now Dark Engergon full Megatron from unleashing Dark Engergon to Cybertron's core.
Detecting a transmision from Sentinel Prime, autobots Jazz and Optimus Prime go to Kaon to save him. Before he dies Sentinel tells Optimus to save the core. Optimus, Bumblebee and Jetfire go to the core avoiding Dark Energon on the way. At the core Bumblebee takes out the Plasma Energy Chamber, and Optimus recieves a mental communication from the core itself, Primus. Now that Dark Energon has stop contaminating the core in which the planet will take centuries to heal itself and during that time will not be able to create enough Energon to surfice the Cybertronian poppulation, To shoe Optimus not to lose hope Primus give him the Matrix of Leadership.
Seeing that the planet will soon be uninhabitable Optimus Prime orders the Ark to be thier new Autobot vessel to venture to find the Allspark. Optimus quickly asks Alpha Trion to come with the autobots in search for the Allspark. Alpha Trion refuses and wants to be with the planet during its demise.
With the Nemisis, the Decepticons battleship ready to venture through space to find the Allspark, Jazz has found an energy signature of the Allspark. Optimus Prime and the Autobots are ready to start there adventure.