The Master Brain is the main antagonist and final boss of the 2016 3DS game Metroid Prime: Federation Force. It is the AI supercomputer in control of the Space Pirate battleship, the Doomseye.
The Doomseye was a massive battleship and the "strategic weapon" used by the Space Pirates in their plan to destroy the Galactic Federation headquarters. Samus Aran was sent to the current location of the Doomseye, in the Bermuda System, to exterminate the Space Pirates, but the Federation loses contact with her. With no other options, the Federation Force were sent to investigate the area. The Doomseye hid its location under cloaking, but the Federation Force destroyed the Transfer Devices on the three planets of the Bermuda System powering the cloak, exposing the Doomseye. The Federation Fleet then opened fire on the Doomseye, but a large energy shield blocked their fire. The Doomseye then unleashes a massive laser, wiping out a majority of the fleet. Coming up with a plan, the Aegis, the mothership of the fleet, distracts the Space Pirates as the Federation Force use small craft to bypass the energy shield and infiltrate the Doomseye and disable the shielding from within.
Inside the Doomseye, the Federation Force discover Samus, having been imprisoned by the Space Pirates. Suddenly, several devices deploy amplification beams at Samus, not only brainwashing her, but increasing her size as well. The Federation Force defeat the amplified Samus by tricking her into ramming her Morph Ball into the electrified wall, and returned to normal. However, she is seemingly crushed by falling debris. Upon reaching the center of the Doomseye, the Federation Force discover the Master Brain controlling the Doomseye as its generator. The Master Brain attempts to summon turrets to fight against the Federation Force and has its force field constantly heal it over the battle, but the Federation Force ultimately overwhelm the organism and destroy the Master Brain.
With the Master Brain destroyed, the Space Pirates lose control over the Doomseye's energy shield, enabling the fleet to attack and ultimately destroy the battleship before it could fire another laser. The Federation Force manage to escape with the help of Samus, but are ejected from the ship and sucked into space. Fortunately, they manage to cling on to Samus' Gunship.
The Master Brain is a large brain-like machine with four white eyes, one on each side of the machine.
- The Master Brain presumably has a connection with Mother Brain.