- Small star
- Smith (Disambiguation)
- Snare Beam
- Snatcher
- Snomer
- Snow hub
- Soh Choong Leong
- Solairon 12
- Solar-energy collector
- Solar Core Harvesting Facility
- Solar lens
- Solomon Aran
- Soma Omori
- Sonia Trepiccioni
- Sonic Boom
- Sonny Santa Maria
- Sophia Remrod
- Soshi Abe
- Souichi Yamamoto
- Sound Test
- Sounds of Dread
- Soundtrack Gallery
- South Core Tunnel
- South Jungle Court
- South Jungle Hall
- South Quarantine Tunnel
- Sova
- Space Decay
- Space Development Corporation
- Space Dragon
- Space Hunter (Disambiguation)
- Space Jump
- Space Jump Boots
- Space Pirate
- Space Pirate/Gallery
- Space Pirate (Disambiguation)
- Space Pirate (Metroid Prime)
- Space Pirate (language)
- Space Pirate ATC
- Space Pirate Assault Skiff
- Space Pirate Boarding Pod
- Space Pirate Command Network
- Space Pirate Crate
- Space Pirate Data
- Space Pirate Deck Commander
- Space Pirate HQ
- Space Pirate Logs
- Space Pirate Mother Ship
- Space Pirate Panic
- Space Pirate Rush
- Space Pirate Science Team
- Space Pirate Sympathisers
- Space Pirate defense shield
- Space Pirate destroyer
- Space Pirate flagship
- Space Pirate mining facility
- Space Pirate portable generator
- Space Pirate starship
- Space Pirate vessel
- Space Pirates (Laboratory Gate)
- Space Pirates (theme)
- Space Research Vessel Marina
- Space Science Academy
- Space Sound
- Space Torch
- Space World 2000 demo
- Spaceport
- Spacetime Beam
- Spaikk bush
- Spawn (Disambiguation)
- Spazer Beam
- Speaking role of Samus Aran
- Special-forces unit
- Special (Disambiguation)
- Special Actions
- Special Charge Beam Attacks
- Special Forces Ship Otowa
- Special Investigations Group
- Special Mission
- Special Move
- Special Token
- Species War
- Specimen Storage
- Specimen catwalk
- Specimen storage room
- Spectral Lock
- Speed Booster
- Speed Booster Hall
- Speed Booster corridor
- Speedrunning
- Spencer Stoddard
- Sphere (Disambiguation)
- Spheres
- Spider (Disambiguation)
- Spider Ball
- Spider Ball Track
- Spider Boost
- Spider Complex
- Spider Guardian
- Spider Magnet
- Spike
- Spike Bomb
- Spin Attack
- Spin Boost
- Spin Jump
- Spin Jump Attack
- Spinner
- Spinning claw
- Spire
- Spire (Disambiguation)
- Spire (theme)
- Spire Dock
- Spires
- Spirit
- Spirit (Disambiguation)
- Spitclawk
- Spittail
- Splinter
- Splinter Cocoon
- Splinter Hive (Disambiguation)
- Splinter Hive (location)
- Splinter Hive (theme)
- Sporb
- Spore
- Spore Spawn
- Spore Spawn Room
- Spring Ball
- Squad Bravo
- Squeept
- Stabilizer (Disambiguation)
- Stacking
- Staff Credit
- Staffroll
- Staging Area
- Stairwell
- Stalactite
- Stalactite cavern
- Standard Air Attack
- Standard Attack
- Standee
- Star Ship
- Star and Screen KOs
- Starshark
- Starship (Metroid Fusion)
- Starship (Zero Mission)
- Stasis Bunker
- Stasis chamber
- Station (Disambiguation)
- Statuary shaft
- Statueroom
- Statues Hallway
- Stealth field generator
- Steambot
- Steambot Barracks
- Steamlord
- Steamlord (theme)
- Steamspider
- Steel orb
- Stefania Montagnese
- Steffen Lotz
- Stephan Weyte
- Stephen Dupree
- Stephen Hughes
- Stephen Ward
- Stephen Zafros
- Steve (Disambiguation)
- Steve Barcia
- Steve Bond
- Steve McCrea
- Steven Brekelmans
- Sticker
- Stiletto-Class Fighter
- Stinglarva
- Stoke
- Stone Statues
- Stone Statues (theme)
- Stone Toad
- Stone creeper
- Stone structure
- Storage A
- Storage B
- Storage C
- Storage Cave
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