Secondary weapons are crucial for dealing heavy damage and solving puzzles.

- Missile: Your standard secondary weapon. Deals high damage to enemies and opens red missile doors.
- Storm Missile: Locks onto up to five targets (or one target five times) and fires a volley of missiles. Excellent for crowd control and specific puzzles.
- Morph Ball Bomb: While in Morph Ball form, drops a small bomb that destroys bomb blocks and damages nearby enemies.
- Cross Bomb: An upgrade to the Morph Ball Bomb, creating a cross-shaped explosion that destroys more blocks and has a wider damage radius.
- Power Bomb: A devastating weapon that clears all enemies and specific Power Bomb blocks on screen, revealing hidden paths and items. Limited in supply.
Mastering these explosives is key to progression and secret hunting.