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| Action | Nintendo GameCube | Wii / Wii U (Metroid Prime Trilogy) | Nintendo Switch (Metroid Prime Remastered) |
|---|---|---|---|
| [Menus] Select item |  / 
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 / 
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 / 
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| [Menus] Confirm item | 
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| [Menus] Cancel | 
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| Move |
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| Jump [During Jump] Space Jump [In Morph Ball mode] Boost Ball Dash sideways while locked-on |
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/ 
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| Shoot beam (Press and hold) Charge [In Morph Ball mode] Bomb |
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/ 
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| Switch visor |
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Hold  + 
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| Switch beam | 
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Hold  +
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Hold  +
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| Turn into Morph Ball / Change back | 
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| Shoot missile (Press and hold the beam button until completely charged) Charge Combo [In Morph Ball mode] Power Bomb |
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| Aim |  +
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| Fix viewpoint | 
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| Lock on [In Scan Visor mode] Scan objects Grapple Beam |
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| [In Morph Ball mode] Spider Ball |
| ||
| Display map screen | 
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| Display pause screen | 
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| Take screenshot | N/A | 
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N/A |
Remastered[edit | edit source]
The Remastered version offers several different control schemes to choose from, including a "Classic" option that mimics the control scheme of the original GameCube version, a "Dual Stick" option that plays similarly to most modern FPS games, and a "Pointer" option that uses the Joy-Cons' motion controls for camera movement and aiming, similar to Metroid Prime: Trilogy for the Wii.
| Dual Stick | Pointer | Hybrid | Classic | Action |
|---|---|---|---|---|
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Move | |||
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Gyro | ( or )+
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Control camera | |
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,
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| ,
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(Morph Ball) Spider Ball | |||
| ,
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| ||
| ,
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| ||
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| ||
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Morph Ball | |||
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Flick Right Joy-Con up | (Morph Ball) Spring Ball | ||
| ,
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Recenter Gyro | |||
| ,
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Gyro Mode | |||
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Combat Visor | |||
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Scan Visor | |||
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Thermal Visor | |||
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X-Ray Visor | |||
| +
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Power Beam | ||
| +
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Wave Beam | ||
| +
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Ice Beam | ||
| +
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Plasma Beam | ||
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Pause Menu | |||
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Map | |||