In the game's Japanese commercials, Samus was portrayed by gravure idol and actress Chisato Morishita, who was hand-picked by the game's director Yoshio Sakamoto for the role. To get into character, she played Metroid Fusion on set, only getting stuck at the game's second boss Zazabi and asking Sakamoto to help her beat it while he supervised the commercial's filming. Sakamoto and Nintendo claimed she was picked for the role because her "gaze" reflected Samus' spirit, willpower, and convictions, while idol magazines at the time strongly felt she was picked for her sex appeal, which was utilized in the commercial. Her image was also used on a "Play Diary" walkthrough on the game's Japanese website, and for prizes in an official Time Trial contest. The fastest 80 players received a two-tone Game Boy Advance SP styled after Samus' Varia Suit and featuring Spoiler:a drawing of Samus, Old Bird and another Chozo seen at the end of the game, while the top 50 received a Samus t-shirt (which was also available through the American magazine "Nintendo Power"). Morishita signed flyers and standees of her appearance in the commercial, which were awarded to the top 10 and top 3 players respectively as grand prizes. As of 2025, the game's Japanese website is still online including sections regarding the Time Trial contest and Play Diary walkthrough, but all uses of her name and image in the walkthrough have since been removed. Morishita retired from the entertainment industry in 2019 and entered a career in politics, eventually being elected to represent the Tōhoku region as a member of Japan's House of Representatives in 2024.

After completing the game, it's revealed that Samus made a small engraving on the base of the Ruins Test boss when she had lived on the planet as a child. The image is of herself, Old Bird, and an unknown Chozo that may represent Gray Voice.

Crocomire was originally going to be in the game, but was cut for unknown reasons. Crocomire can still be accessed by hacking into the game's code, but the existing animations are seemingly unfinished and there's no death sequence.