Supreme commanders were the right hand of their Harvester Queens, and had their own Colony ships to prove it. They specialized in commanding invasions, coordinated attacks, and traps.
The supreme commander from Independence Day was exceeding expectations in all of these, shown when he trapped David and Steven in the Colony ship when they were infiltrating it, destroyed numerous cites at once using satellites to relay a timer, and the massive battalions we see about board their ships when David and Steven were trapped.
They also have the pivotal role of becoming temporary leaders for their colonies if their Queen died, but this would only last until they found another Harvester Queen to lead their forces.
A Supreme Commander's suit is bigger than then the regular one for smaller Harvesters, and even has its own seat inside. The supreme commander inside was connected to his colony ship via a computer screen in the suit. The commanders' suit did not have a gun attachment, but could manually fire it using the suits hands. The suits also had light blue patches on it, so they could be notified as Supreme Commanders from afar.
War of 1996
On July 2, 1996, a Supreme Commander was sent by his Queen to invade Earth with his Colony ship, hidden behind the Moon and using Earth's man-made satellites to transmit a countdown signal to when he and his Harvesters were to attack. The Supreme Commander also sent down City destroyers to Earth's major cities, including Los Angeles, New York City, and Washington, D.C., and when the countdown signal has reached the deadline, the Queen orders the destruction. The Supreme Commander follows her orders, and major cities across the globe were demolished.
On July 4, 1996, the Supreme Commander gets his orders from the Queen to attack Area 51. However, Captain Steven Hiller and David Levinson take a captured Attacker. They get into the Colony ship, where they upload a virus into the central computer of the Colony ship, render all Harvester spacecraft from the Colony ship to be vulnerable to firepower by the military. This allows several planes (led by President Thomas Whitmore, who was a combat pilot himself) to take down the City destroyer in order to save Area 51 and its occupants.
However, as Hiller and Levinson are about to leave, he soon learns about their presence, but they fire a nuke to the Colony ship's core before making a close escape. This causes the Colony ship to finally explode, killing the Supreme Commander and the remaining Harvesters on-board.