The Great War was the first and most violent outburst of fighting on the planet Cybertron between the Autobots and Decepticons. It began when Megatronus started his initial drive to overthrow the Caste system. Megatron's noble goal of being a Prime was corrupted by his jealousy over his friend Orion Pax, who being named the next Prime. This set the spark in the war and the Golden Age became history over time.
Fighting between the two factions lasted for several million stellar cycles, not even those who chose to be Neutral could avoid the war. Near the end, Cybertron was a barren, lifeless wasteland, devoid of Energon, forcing Optimus Prime to enact the Great Exodus, a mass evacuation of all Cybertronians to leave their dying world and find other worlds to seek refuge.
After the War on Cybertron, Optimus Prime went with his Team to Earth where they faced another battle against the Decepticons. The war came to a close when Megatron was killed by the Autobot scout, Bumblebee. After reclaiming the AllSpark, Optimus returns to Cybertron to find Unicron attacking the planet, and seals the Chaos Bringer away. Optimus sacrifices himself to restore the AllSpark to the Core of the planet, while a revived Megatron dissolves the Decepticon movement.
- Orion Pax is appointed Prime by the High Council. Megatron kills counsellor Halogen in anger, sparking tensions between the two former friends.
- Fort Scyk is taken by the Decepticons, overwhelming the unprepared and lazy garrison stationed there. A regiment of Council Guardians ultimately turns the tide, led by Ultra Magnus.
- The Hydrax Plateau is seized by the Decepticons; with this key feature captured the majority of Cybertron's eastern hemisphere falls to the Decepticons and remains as such for the remainder of the war.
- The Satellite Command Center at Polyhex is taken over by Decepticons.
- Crystal City is razed, primarily by Constructicons, using their "Devastator" gestalt modes for the first time. Though the Autobots fight hard, the city is ultimately destroyed, though many of its scientific treasures escape or survive the collapse.
- The Autobots win their first major victory of the Great War at Kalis, primarily due to a lack of Decepticon air support. The Autobots begin to use long-range combat as a primary tactical advantage. Bruticus Maximus is defeated by Sideswipe, Jazz, and Optimus Prime. Kalis remains in Autobot hands.
- The cities of Tarn and Vos are occupied by Shockwave's forces; the Decepticon turns the two cities against one another, resulting in Tarn's destruction. Vos is destroyed not long afterwards through Shockwave's machinations, crippling Starscream's power base and allowing the mad scientist to position himself as second-in-command.
- The Autobots and Decepticons battle at Praxus. The city-state is ultimately leveled by the fighting, and to this day the outcome is unclear. Prowl and Ironhide, citizens of Praxus, join the Autobot cause.
- Bruticus Maximus leads a massacre at Nova Cronum, killing every sentient being there. Megatron sets up a fortified command post among the ruins.
- The Tagan Heights are demolished by years of fighting. It is here that the Wreckers prove crucial to the Autobot war effort, and the Autobots manage to create their own combiner, Defensor, who fights a Devastator to a standstill.
- After centuries of stasis, the AllSpark creates a final generation of Transformers, most of whom side with the Autobots.
- The AllSpark is ejected from Cybertron. A standstill ensues.
- Seeking a new edge in the war, Megatron storms Trypticon Station and wrests control of it from Starscream, empowering himself and other Decepticons with the Dark Energon stored there.
- The Seekers travel deep underneath Cybertron in search of the long-abandoned Geosynchronous Energon Bridge beneath the ruins of Crystal City, which will allow the manufacture of new Dark Energon for the Decepticons' use.
- Megatron leads a final attack on Iacon and attempt to travel to Cybertron's core. Though Sentinel Zeta Prime and Omega Supreme stand in his way, the Decepticons defeat them both. Because of this, the Decepticon leader manages to reach Cybertron's core and corrupt it with Dark Energon—a critical blow against the Autobots.
- The Autobots manage to drive the Decepticons from Iacon. Optimus and his inner circle lead a raid on the prison, but they cannot save Sentinel. Optimus now truly assumes leadership of the Autobot cause.
- Heading down through Cybertron's inner layers, Optimus finds much of the planet to have been thoroughly infected. Optimus is given the Matrix of Leadership by the Core, a fragment of Prima's powerful sword that contains a portion of Cybertron's spark.
- Optimus orders the Great Exodus of all Cybertronians, though a small portion of the Autobots stay behind under his direct command, and the same transpires for Megatron's Decepticons. Exodus War for Cybertron During the exodus' final days, Megatron is temporarily killed by the mighty Metroplex until he is revived by Soundwave. The Autobots depart Cybertron in the Arkwhile the Decepticons do so in the Nemesis. Some stay behind, including Shockwave, the Dinobots, and Ultra Magnus and his
- After several adventures through the cosmos, Optimus clashes with Megatron on Earth, following which, the Decepticon leader departs into space to search for an army. While the Autobots ally themselves with the United States of America, Starscream is left in command and lays low, leaving the smaller conflict stagnant until he kills Cliffjumper three years into their stay on Earth. Three human children, Jack Darby, Miko Nakadai, and Raf Esquivel are caught up in the conflict and become members of Optimus' unit. Megatron soon returns and brings Dark Energon to Earth, officially renewing the war.
- The Autobots and Decepticons ally to defeat Unicron, who is revealed to be Earth's core.
- After a lengthy arms race over relics scattered on Earth, both factions battle over the right to revive Cybertron through the Omega Lock, but when forced into a corner, Optimus destroys it, dooming Cybertron to remain lifeless. The Autobots are dealt a crushing defeat by Megatron in retaliation, but eventually successfully regain lost ground when Ultra Magnus arrives on Earth.
- On the verge of creating a new army of cloned Predacons, the Decepticons lose more than half of their military strength thanks to a mishap involving a Terrorcon infestation, severely weakening their war effort. Thirst This coupled with Predaking revealing his sentience causes Megatron to terminate the cloning scheme, and he resolves to repair the Omega Lock.
- When the Omega Lock is completed, the Autobots attack the Nemesis, killing Megatron and reviving Cybertron, effectively ending the Great War with an Autobot victory. Deadlock After reclaiming the AllSpark, Optimus returns to Cybertron to find Unicron attacking the planet, and seals the Chaos Bringer away. Optimus sacrifices himself to restore the AllSpark to the Core of the planet, while a revived Megatron dissolves the Decepticon movement.
- Battle for Fort Scyk
- Siege of Hydrax Plateau
- Fall of Crystal City
- Defense of Kalis
- Destruction of Tarn and Vos
- Battle of Praxus
- Nova Cronum Massacre
- Battle for the Tagan Heights
- Dark Energon Crisis
- Battle of Tyger Pax
- Search for the Dark Spark
- Pre-Exodus Campaign
- Great Exodus
- Darkmount, NV Skirmish