After Optimus Prime removed the core's Dark Energon infection, a voice informed him that they had to leave the planet as it healed, and gave him the Matrix of Leadership. Optimus returned and initiated Project Generation One, a project that Jazz rechristened the Ark. Alpha Trion oversaw construction of the ship in the Well of All Sparks, while Optimus led a distraction by having the Aerialbots gather every available ship. The Autobots flew these ships towards the last surviving space bridge in Cybertron's orbit, drawing out Trypticon. The fleet dispersed while Optimus's crew guided the Eight Track to a blind spot on Trypticon, boarding the station and fighting through to the Spark Chamber, firing at it and causing Trypticon to crash.
As Optimus's crew returned to a completed Ark, it emerged Trypticon had survived and was heading for Iacon. Jetfire and Springer gave up a place to buy time, and soon Ultra Magnus and his Wreckers also gave up a place. Ratchet informed Prime and Magnus that Omega Supreme would also be nobly refusing a seat. Trion refused to board the Ark, explaining he would find refuge with Vector Sigma. As the Ark took off while Decepticon forces flooded Iacon, Trypticon transformed into the Nemesis. Megatron and his elite warriors boarded the ship and gave pursuit, while Shockwave took command of the Cybertronian Decepticons. The Ark and the Nemesis entered the last space bridge, but were distributed to different parts of space.
During the Autobot evacuation, Megatron messaged Optimus and Ratchet that he was punishing them for their defiance, and Trypticon began firing on the ships. Optimus ordered Silverbolt, Jetfire and Air Raid to disable the station. Before Trypticon could locate Optimus Prime and destroy him, the airborne Autobots attacked Trypticon, damaging him during transformation, and causing him to fall to the planet. At the planet's surface, Optimus, Ironhide and Bumblebee defeated the massive Decepticon. Afterwards, Optimus gathered his comrades and showed them the Ark under construction, and declared they would leave aboard it once Megatron was stopped.
Many years after Optimus Prime had given the order to evacuate Cybertron, the majority of Autobots and Decepticons alike had left the planet. The Ark was the Autobots' last ship, meant to transport Optimus and his core team away from the dying planet. However, Megatron would have none of it, and launched an assault on the Ark that drained the Autobots' Energon supplies and would've doomed them had Optimus not awoken the titanic Metroplex, who swiftly turned the tide and crushed Megatron to death. Starscream assumed command of the Decepticons, while Jazz and Cliffjumper were sent to the Sea of Rust to find the missing Grimlock. In a tomb of the Ancients, Cliffjumper discovered a holographic star map that pointed to Earth, which Shockwave had pinpointed to loot its resources using a space bridge to repair Cybertron. The two Autobots claimed the Energon for the Autobots, only for the Combaticons to take it back. Megatron, having been covertly repaired by Soundwave, deposed Starscream, who had blown the Decepticons' entire Energon supply in his disastrous failure of a regime, necessitating the Decepticons to evacuate the planet. Megatron transformed Trypticon's carcass into the Nemesis to make his escape to Earth with through Shockwave's space bridge, until Grimlock was able to destroy the tower that had created it. With no other options, Metroplex sacrificed his life and Energon to fuel the Ark's departure from Cybertron. The Ark subsequently engaged the Nemesis in a lengthy battle, but both ships were haphazardly sucked into the collapsing space bridge. Wherever they may have gone, the Autobots and Decepticons achieved their mission and ended the Great Exodus, leaving Cybertron a quiet, lifeless husk.
- The term Great Exodus is given twice in 2011's Transformers Hall of Fame profiles, mentioning that Shockwave stayed behind, and Jazz went with Prime on the Ark.