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(written from a Production point of view)
Star Trek: 25th Anniversary is a game for the Game Boy. The United Federation of Planets detected the planet killer three months prior to the game. Federation Engineers began working on the Proto-Matter Fusion Disruptor, the only device capable of stopping the machine. When the Doomsday Machine entered Federation space, the machine was being installed on the USS Excalibur and be taken to Sector Alpha 9, where the Planet Killer was located.
However, the Klingon Empire heard of the Disruptor's existence and intercepted the Excalibur because they feared the use of it on the Empire. After stealing it, they broke it into 12 pieces and hid them on several different worlds. Admiral McQuilkin of Starbase 4 requested James T. Kirk to find the pieces and stop the machine. Kirk did this and beat the Doomsday Machine.