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Mother Brain (マザーブレイン?) is the monstrous battle theme for the boss of the same name in Super Metroid. Playing during the Final Conflict, this theme shares the same melody and harmony for the original Zebetite theme, Mother Brain's theme in Metroid and Metroid: Zero Mission. Mother Brain is also similar to the Parasite Queen's music in the first Metroid Prime. The theme is included on the Super Metroid: Sound in Action soundtrack, as well as Play it Loud! Original Soundtrack Volume 1, a compilation SNES album offered by Nintendo Power in 1996.

In 2011, the theme was performed by live orchestra as part of the Metroid arrangement in PLAY! A Video Game Symphony. In 2013, the theme was arranged by the WDR Radio Orchestra as part of Into Red, Into Dark and received a fuller reprise later in the medley.

The original theme can be heard here.