It is a red, blue, green and gold arm chair with control panels fitted onto each arm. Whenever he sits on it, he detaches his legs so his body can fit comfortably into the ring shaped seat of it. When seated, he can hover and fly at 20 feet with perfect maneuverability.
The control panels on each side of the throne have many different functions. At the touch of a button, Megabyte can activate his Tor's machinery, access the built in computer and open VidWindows at any point in Mainframe and Lost Angles either for information or a way of communication. (The Tearing) (The Medusa Bug) (In the Belly of the Beast)
He can also open a concealed platform under the floor of his throne room that contains his legs when he wants to reattach them. (Quick and the Fed)
Manual control is sometimes activated when he wants to take full control of anything outside the Tor. This was shown when he ordered Mouse after she accidentally ended up in Enzo Matrix's body instead of Bob's to give him full control so that he could steer him to the core of the Principal Office. (The Great Brain Robbery)
Megabyte also can activate weapons on his throne consisting of missile launchers and machine gun barrels. This was shown when he first battled Bob and used his throne to defend himself. He could also activate turrents. (ReBoot: Countdown to Chaos)
When the Tor was destroyed by Hexadecimal, Megabyte relocated to the Principle Office taking his throne with him. After he was defeated and Mainframe was reformatted, it is assumed that it was erased along with his Tor. (Megaframe) (End Prog)