Built around the undersea crash site of their former starship, Decepticon Headquarters served as the main base of operations for Megatron's troops on Earth. The base included several new buildings, and a docking tower, a giant telescoping "elevator" which allowed the Decepticons to reach the surface without having to get wet and risk getting rusty.
The Transformers cartoon
In the months after the Decepticons' new space cruiser crashed into the ocean, they built several buildings around it to serve as their main base.
Being located underwater, Decepticon Headquarters was quite prone to flooding; its walls were breached on at least four known occasions. The first was due to enemy action. The Decepticons had kidnapped Sparkplug Witwicky; in the process of rescuing him, Cliffjumper used his glass-gas to burn a hole in the base. Brawn later punched another hole in the wall before the Autobots made their escape.
When the Decepticons used the space bridge to move Cybertron to Earth's orbit, it caused massive natural disasters which the Decepticons hoped to make Energon with. Unfortunately, the space cruiser was damaged, with rocks from a nearby extension falling on the base and breaching the hull. Also, the docking tower snapped in half due to a tidal wave, flooding much of the base. That's what happens when Rumble is responsible for material acquisition. The Decepticons spent some time repairing the damage and cleaning up the flooding.
When Carly allied herself with the Autobots, she took it upon herself to sabotage Decepticon Headquarters, placing bombs on the hull. Unfortunately, when it went off, she had been captured and placed in the very room that was being flooded. The Decepticons sealed off the rest of the base, keeping it dry, and left the human to drown, unaware that Ironhide rescued her.
Later, after the Sky Platform, a hovering energy collecting station built by the Constructicons, was lost, the Decepticons fled back to the space cruiser. However, Powerglide directed the station to sink directly above the space cruiser's location. Megatron ordered Soundwave to activate the base's force fields, only to learn that the Decepticons had never installed force fields. As the station came crashing down, Megatron assigned the Decepticons to their most difficult task to date...clean up the mess the station's impact had made of the base. They probably made Starscream do it.
It is unknown what happened to the base when the Decepticons fully conquered Cybertron and abandoned Earth.