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It is remixed in Metroid: Zero Mission, and used once again for the battle against Kraid. The theme in Zero Mission features a short introductory flourish when Samus steps into Kraid's chamber before flowing into the main theme. Notably, it also features piano strokes common in Metroid Fusion themes such as Sector 4 (AQA) Aquatic Control Level Area. The theme is included in the Sound Test as number 09.
It is one of two "Big Boss Confrontation BGM" themes, the other, used for Ridley and Draygon (and the escape sequences), would be titled "Vs. Ridley" in later years, becoming Ridley's signature battle music. The Mogenar boss and battle theme in Metroid Prime 3: Corruption resembles both Kraid and the Big Boss Confrontation BGM theme, and may have been intended as an homage.
In 2013, the theme was arranged by the WDR Radio Orchestra as part of Into Red, Into Dark.