Later on, Autobot City was (presumably) modified and rebuilt into Metroplex who was also able to transform into a more conventional humanoid mode. Trypticon, in his first mission after destroying the Ark, attempted to destroy Metroplex. Although Metroplex was initially unable to transform, his transformation cog was replaced at the last minute, allowing him to take on a robot mode. Metroplex won the fight easily, tossing Trypticon into the ocean. Some time later, the ghost of Starscream helped Scourge to infiltrate Metroplex and steal his optical units (eyes). One was successfully stolen, while the other was destroyed in the attempt.
In 2004, Autobot City was officially opened. Shockwave, annoyed at having to serve once more under Megatron, launched an air assault to kill the humans and wreck the alliance. It was foiled due to the illogical (and therefore unplanned for) actions of Hot Rod, one of the city's defenders.
In late 2005, Megatron launched an all-out assault on Autobot City. Though it ultimately failed to destroy the city, heavy damage was sustained, and Optimus Prime was killed. In 2008, the Quintessons invaded and captured the city itself, but its living core, Metroplex, rose up from beneath the city and wiped out their entire fleet.