This article is about the last enemy fought in Metroid Prime: Federation Force. For the similar character on Zebes named Master Brain in NES scratch-it cards, see Mother Brain.

Master Brain is a brain-like organism at the center of the Space Pirate ship Doomseye. In the climax of Metroid Prime: Federation Force, the Federation Force infiltrates the Doomseye to destroy its Force Field generator from within, which they discover is the Master Brain.

Master Brain will summon Grim-Class Turrets around itself. There is a pink force field that surrounds it; while it does not protect the Master Brain from attacks, it instead slowly heals the Brain throughout the battle. The Federation Force is thus required to damage the boss faster than the field can heal it. Once it is destroyed, the Doomseye loses its shield, and the Federation Fleet begins their attack.


  • The game offers no information regarding Master Brain, and its origins are never explained. Based on the name alone, it can be assumed to have a connection to Mother Brain, the leader of the Space Pirates. Unlike the latter, however, Master Brain has a far less significant role, as it is simply deemed a generator to the Doomseye's shield.
  • It may also have a link to the Federation's Aurora Units, who themselves have an unknown relation to Mother Brain. The Master Brain's mechanical appearance gives it a stronger similarity to an AU, possibly making it a Pirate-based Aurora Unit or a stolen and compromised Federation AU. The latter theory would draw strong parallels to the stolen Aurora Unit 313.
  • The robotic voice heard prior to the battle against Samus Aran in Federation Force may be from Master Brain itself, due to the symbol appearing next to the text dialogue being visually similar to the boss.
  • The Master Brain battle is very similar to the Mother Brain battle in the original Metroid game. Both bosses do not directly attack themselves and instead solely rely on turrets (although unlike Mother's Cannons, Grim-Class Turrets can be destroyed). Both bosses' destruction also lead to a countdown.
  • Mother Brain was referred to as "Master Brain" in the Topps scratch-off card Screen 9 of 9.