These special abilities consume Aeion energy for powerful effects.

- Phantom Cloak: Renders Samus invisible to enemies (including E.M.M.I.) and bypasses motion sensors. Consumes Aeion energy rapidly.
- Flash Shift: Allows Samus to dash quickly a short distance horizontally, up to three times consecutively. Excellent for evasion and quick traversal.
- Pulse Radar: Emits a pulse that reveals hidden blocks and items in the immediate vicinity. Consumes Aeion energy.
- Storm Missile: (Also listed under Missiles, but uses Aeion for multi-lock-on functionality)
Strategic use of Aeion abilities is vital for survival and uncovering secrets.