The nature of the villainous Mother Brain has been a matter of debate for years. In the original game's instruction manual and in-game texts, she is identified as the absolute leader of the Space Pirates, and the mastermind of their plans. The manual even goes as far as saying that Ridley and the Space Pirates are completely under Mother Brain's mind control. The manual of Metroid: Fusion (2002) and the in-game introduction of Super Metroid (1994) also name Mother Brain as the leader. However, the instruction manuals of Super Metroid and the remake Metroid: Zero Mission (2004) clearly name Ridley as the Space Pirates' general and leader, with Mother Brain being merely the computer that controls their defenses. Metroid Prime (2002) first made mention of the Space Pirates High Command, and the Metroid Manga (which was only officially released in Japan prior to the release of Metroid: Zero Mission) sheds further light on this: it identifies Mother Brain as a highly advanced artificial intelligence, created by the Chozo years before. This A.I., who also supervised Samus Aran during her childhood on Zebeth, eventually outgrew her makers in intelligence, and betrayed them by helping the Space Pirates conquer the planet. The manga unequivocally clarifies that Ridley is the Space Pirates' leader, and that their quest for dominance started long before they ever got into contact with Mother Brain; however, Mother Brain has since manipulated both Ridley and the Pirates into working for her, to further her own goals.
This game is a remake of the original NES Metroid (1986) and is Samus Aran's first official mission on Zebes. Unlike previous titles, the game adds in additional storyline elements following the defeat of Mother Brain. The planet setting is also somewhat different from Metroid and Super Metroid, yet it retains many similarities.
Crocomire, the large miniboss from Super Metroid (1994), was supposed to be in the game, but this never happened for unknown reasons. Data can still be found in the game's code that show him looking much less scarred than in Super Metroid, suggesting that this early encounter with Samus would explain his later, much rugged appearance in Super Metroid.