During a unique segment of the game, Samus loses her Power Suit and must navigate the Chōzōru Ruins and Space Pirate mothership in her vulnerable Zero Suit. In this form, Samus is agile and can crawl through small spaces, but she has no defensive capabilities and only a weak stun pistol for offense. This 'build' emphasizes stealth, evasion, and puzzle-solving.

Playing as Zero Suit Samus requires a complete shift in strategy. Direct confrontation is almost always fatal. Instead, you must use her agility to jump over obstacles, crawl through vents to bypass enemies, and use the stun pistol strategically to create openings. This segment highlights Samus's resourcefulness and provides a fresh gameplay experience, showcasing her abilities even without her iconic suit.