The Ark served as the base for the Autobots for years, while Autobot City was being planned and built. Its computer, Teletran-1, served as their main source of computing power and communications ability. In 2006, Trypticon attacked and destroyed the Ark, making Autobot City (aka Metroplex?) their sole headquarters.
Believing themselves fully energized, the Decepticons attacked the Ark, pushing aside the Autobot resistance with relative ease. However, it turned out the fuel was poisoned, and it was Shockwave, who didn't use this fuel, who succeeded in defeating the Autobots and capturing the Ark. Ratchet, who wasn't aboard the Ark at the time, tried to sneak in while Megatron was the only one guarding it. Megatron caught him, but instead of destroying him, he made a deal with him for the death of Shockwave. Ratchet instead revived the Dinobots, and got Megatron away from the Ark long enough to revive the captured Autobots too. Once again, the Ark was under Autobot control.
When Grimlock became leader, the Ark was repaired, refueled, and launched into space. There, it continued to serve as Autobot Headquarters for over two years, although part of that time was spent disabled on the moon's surface. During its stay in space, the Ark was used to ferry the combined Autobot-Decepticon army to Earth, after Starscream destroyed both Decepticon motherships following exposure to the Underbase.
During the Transformers' battle with Unicron, the Ark was used by Grimlock to sideswipe Unicron's head, damaging the ship greatly. Following this, the Ark was stolen by Shockwave and Starscream, unaware that Ratchet, Megatron, and Galvatron were aboard. While heading for Earth, a fight broke out between Starscream and Ratchet. The doctor, psionically joined to Megatron, deflected a shot meant for him into a console. The Ark, out of control, was caught in the Earth's gravity well and plunged into northern Canada.
Megatron eventually gained control of the Ark and offered to trade its technology to Cobra for a new body. However, only a tiny portion was unloaded before Megatron unexpectedly launched the ship. Stowed away onboard the Ark were Fortress Maximus and Skydive, there to stop Megatron and rescue the captive Dr. Biggles-Jones. Realizing the impossibility of defeating Megatron, Fortress Maximus threw himself into the ship's reactor core. The resulting exposion didn't succeed in killing Megatron, but it did all but disintegrate the Ark.