The Mothership in Independence Day are massive command vessels. They are controlled by the Harvester Supreme Commanders that take their orders directly from Harvester Queens.
A Colony Mothership is of considerable size: it is almost 600 kilometers long across its longest axis (length) and 550 kilometers along its shortest (height). It is made up of two visible portions: an irregular dome on top, and two flipper-like appendages that hang beneath.
The outside resembles to overlapping fields of stilled lava, with a thin blue shield around it. It maintained 83 City Destroyers and probably millions of Harvesters.
There are many tunnels that led to the inside of the ship, of which at least one had a triangle-shaped form. It was through this one that Steven and David were led to the center of the mothership. The deeper into the ship, the more intense the blue mist became (The blue mist might be some sort of gas that helps the Harvesters to breath). There are many different kinds of ships flying through the tunnels and a few are seen by Steve and David.
The center of the ship lies in a thick blue mist. The first part are the multiple towers that surround the centre. The second part is a plateau of eighty kilometers long on which armies of thousands (possibly millions) of Harvesters were preparing for the invasion of Earth. Above this plateau there is a long beehive-like structure which is the main transportation center of the ship. This is the place where Steven and David were led to. This structure has thousands of openings, and out of each openings comes a strong light. These are control rooms in which the aliens control the arrival and departure of the thousands of Attacker fighters. Through long structures they connect the fighters with the Colony ship. At the core of this structure was the main control and command center where hundreds of alien technicians monitored the ship's various functions along with their invasion.
War of 1996
In 1996, a Harvester Queen sent a mothership to Earth, and causing the events of the War of 1996. Throughout the duration of the conflict, the mothership hid behind the Moo], making it almost impossible for humanity to observe it. However, Steven Hiller and David Levinson infiltrated the vessel with a captured alien spacecraft and disabled the force-fields of the City Destroyers. Thereafter, the infiltrators detonated a nuclear missile inside the ship which completely destroyed it. Burning pieces came crashing down to Earth, creating multiple falling stars for those on the planet looking up.