After the battle of Los Angeles, the Autobots gathered their dead and dying. Worldwide they all returned to the Ark to decide what to do next. Prowl was unanimously elected leader, but he vowed that Optimus Prime would live again.
Many Autobots that were damaged were rebuilt into more functional modes instead of disguise oriented modes. Ironhide was rebuilt into a six wheeled armored personnel carrier. Warpath was rebuilt into a newer stronger tank. Hot Spot was rebuilt in his fire truck mode but now it was red. After his rebirth, he renamed himself, Fire Chief.
One day the Ark begin to shake violently. Trypticon was attacking. He was just battering the ancient volcano walls with his bare claws. The remaining Dinobots, Defensor, and other Autobot warriors engaged him, and drove him away, but not without the loss of Jazz, Gears, Windcharger and Omega Supreme. It was later discovered that there was a cave-in at the repair bay and Ratchet, Wheeljack, and Perceptor were crushed, as well as Autobots that they were repairing. The Ark was in ruin.
Prowl decided to relocate the Autobots from Tokyo, New York, and the volcano to an abandoned American military base in New Mexico. The Ark would be salvaged, and all of the Autobots would hide out there until they could mount a suitable defense against the whole Decepticon army.
Prowl concluded that if new Decepticons were in Earths neighborhood, some Autobots might be too. Prowl had Blaster and Eject design a signal for assistance, and transmit it.
The Autobots would try to hold out, but their options were running out. The human civilization was drastically exterminated with very few survivors. Almost every major city on Earth was in ruin. The Autobots could no longer count on much human assistance.
It was soon discovered that all the Decepticons had abandoned the Earth. A new Autobase named Omega would be built. All went well, the Autobots were in a supreme fortress remeniscent of the old Cybertronian dome cities, only underground.
The Autobots with Raoul, Carly and Spike Witwicky were assisting the humans in rebuilding their civilization. All was going well, until the distress call was answered by some very Strange Visitors.
