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Missiles
There are 49 Missile expansions containing an additional 5 slots each. I am not counting the first one as it is unavoidable. The max capacity of the Missile launcher is 250.
Tallon Overworld
Transport Tunnel B - Below the bridge.
Landing Site - Behind the ship in a Morphball-accessible crack.
Overgrown Cavern - Take the bomb tunnel in the save room near the Reflecting Pool in Chozo Ruins.
Frigate Crash Site - In the middle of the lake, double jump from the roots with the Gravity Suit.
Biohazard Containment - Behind a Super Missile door in the very beginning of the crashed frigate.
Life Grove Tunnel - Use a power bomb at the top of the half-pipe.
Great Tree Chamber - Use the X-Ray visor to utilize an invisible platform in the Great Tree Hall.
Root Cave - Use the X-Ray visor in combination with the Grapple beam to swing to the hole.
Arbor Chamber - At the top of Root Cave use the Grapple Beam and X-Ray visor to see the hidden platforms. The Missile door leads to the Arbor Chamber
Chozo Ruins
Ruined Gallery - Shoot the weak wall near the floor with a missile.
Watery Hall Access - Use a missile on the weak wall.
Burn Dome - Morphball bomb the wall in the water.
Ruined Nursery - Traverse the Morphball maze.
Ruined Gallery - Bomb jump up to one of the holes in the walls and roll through.
Ruined Shrine - Morphball bomb the circle in the wall.
Dynamo - Morphball bomb next to the charge beam and blow up the gate with a missile.
Vault - Open the gates in front of the switches with bombs, than activate all three with the Morphball. Double bomb jump to reach the highest one.
Ruined Shrine - Use the boost ball on the half-pipe.
Main Plaza - Use the boost ball on the half-pipe.
Gathering Hall - Morphball bomb the grate on the ledge above the Energy Core entrance.
Main Plaza - Use a super missile on the weak part of the tree, and jump through from above.
Ruined Fountain - Use the Morphball in the fountain, then spider ball across the ceiling.
Dynamo - Use the spider ball track.
Crossway - Use super missiles on the wall hanging to expose a scan that turns on the spider ball tracks. Use them to activate an elevator.
Watery Hall - Jump on top of the ledge on the other side of the Morphball chute under the water. Requires Gravity Suit.
Furnace - Use a power bomb and utilize the exposed half-pipe.
Training Chamber Access - Use the grapple beam to cross the magma pool, and roll through some leaves on the other edge into a hidden tunnel.
Main Plaza - From the Ruined Fountain, take the door to the Magma Pool and keep going until you reach the Main Plaza. Swing across with the grapple beam.
Magmoor Caverns
Storage Cavern - Roll underneath the grating in the Triclops Pit.
Fiery Shores - Clear the boxes after rolling through the first Morphball tube, then traverse the paths on the ceiling.
Triclops Pit - Use the hidden platforms with the X-Ray visor and then use a Super Missile on the pillar.
Phendrana Drifts
Research Lab Aether - Near the very top there are some catwalks for the Morphball.
Research Lab Hydra - Blast the pillar made of cordite with a Super Missile.
Ice Ruins East - Use the Spider ball on the Spider ball track.
Phendrana Shorelines - Blast the wall hanging with a super missile, and scan the inside to turn on a Spider Ball track.
Frost Cave - Use the grapple beam on the Glider and drop off on the ledge with two crates, then shoot the stalactite and go into the exposed water.
Quarantine Monitor - Use the spider ball track in Quarantine Cave up to the ledge, swing across with the grapple beam, and roll to the room.
Phendrana Shorelines - There is an expansion visible inside an icy part of a pillar. Melt it with the Plasma Beam.
Ice Ruins East - Melt the wall of ice with the Plasma Beam.
Gravity Chamber - Melt the icicles on the ceiling with the Plasma Beam, and then use the exposed grapple point to swing across.
Phazon Mines
Main Quarry - At the top of the platforms use the Thermal Visor to activate a Power Conduit and then roll across the new spider ball track.
Elite Research - At the top of the room, turn the cannon to the left side of the room and fire it to bust open the wall.
Elite Control Access - Shoot the box near the vent near the ceiling to open both.
Security Access A - Use a Power Bomb on the gate on the wall.
Phazon Processing Center - A little way up are some invisible platforms, use the X-Ray visor to cross to the ledge and then a power bomb to blow up the wall on the ledge.
Metroid Quarantine A - Power bomb the walls near the spider ball track and roll across the track then use the invisible elevator (X-ray visor).
Fungal Hall Access - Roll underneath the large mushroom at the bottom of the shaft.
Fungal Hall B - Power Bomb the circle of mushrooms right near the entrance.
Metroid Quarantine B - Use a Super Missile on the canister after passing the force field.
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