The Great War began when Megatron gathered a large number of followers, who dubbed themselves the Decepticons, in response to the corruption practiced by the ruling class of Cybertron. As time passed however, it became clear that Megatron only served his own powerlust, plunging Cybertron into war for control of the planet. One of the opening acts of the war was Megatron murdering the High Council.
Early on in the war, some of Cybertron's colonies, such as Caminus, were untouched by the conflict, prompting Chromia to try and have Windblade return home.
Well into the war, Megatron conspired to use Vector Sigma to reprogram the AllSpark and have it birth an endless legion of Decepticons, only for the Autobots to launch the artifact off Cybertron. As a result of this, Cybertron's condition began to decline, prompting Optimus Prime to commission the Ark so the Autobots could locate the AllSpark and bring it home.
Some 66 million years later, the Great War seemed to have turned into a more "cold war" state, at least from the Decepticons' point of view, with the Autobots reduced to a small resistance on Cybertron as the Decepticon fleet travelled the galaxy in search of the AllSpark.