It consisted of a central spire that served as the headquarters with numerous Cybertronian buildings around it. The central spire contained the control mechanisms for the cities various remote controlled machines like battle taxis and helicopters. The highest point of the tower also held the severed arm and gun of Optimus Prime which served as a turret... what an evil plan...
That may or may not be a sign of the coming of the rapture.
The Transformers cartoon
Megatron and the Constructicons developed a secret base beneath New York City where they began extensive operations as laid out by Scrapper's plans in order to create a new base of operations for the Decepticons on Earth. This involved digging and sinking various buildings such as the Empire State Building which was replaced with a central spire that served as central command and control for the Decepticon forces.
Much of New Cybertron was damaged by the Autobots and it was presumably dismantled by the end of the episode.