Shining Ray[edit]
- Obtained from: Optic Sunflower
Fires a starburst projectile straight up which explodes to shoot beams of light in eight directions. The charged shot fires several such starbursts all around.
Squeeze Bomb[edit]
- Obtained from: Gravity Antonion
Fires a purple orb that expands as it moves forward to damage enemies and suck in enemy fire. The charged shot creates a large orb that fills the screen.
Shadow Runner[edit]
- Obtained from: Dark Mantis
Fires a black projectile that homes in on enemies. If there are no enemies around, it returns to X, and he recovers the weapon energy spent on it. The charged shot fires six such projectiles.
Thunder Dancer[edit]
- Obtained from: Gigavolt Man-O-War
Fires a short bolt of electricity that homes in on nearby enemies, and spreads from one enemy to another. The charged shot fires a more powerful bolt.
Melt Creeper[edit]
- Obtained from: Burn Rooster
Releases a wave of fire that travels along the ground. The charged shot sends out two waves, one forwards and one backwards. This weapon only works on the ground.
Drift Diamond[edit]
- Obtained from: Avalanche Yeti
Fires two ice projectiles forward, one diagonally up, the other diagonally down. This can freeze enemies. The charged shot creates a shield of ice shots that revolve around X to hit nearby enemies.
Crystal Wall[edit]
- Obtained from: Earthrock Trilobyte
Summons a crystalline barrier that rises out of the ground, which damages enemies who run into it. This can be used as a shield. Run into it to knock it over, and it damages enemies if it lands on them. The charged shot produces a larger barrier which will sometimes have an item inside. Knock it over to retrieve the item. Using this in certain places can unearth Rare Metals.
Green Spinner[edit]
- Obtained from: Bamboo Pandamonium
Fires a missile that explodes on contact with a wall. The charged shot launches a missile straight up, and then four large missiles come down around X and explode upon landing.
X-Drive[edit]
This weapon is only available when the Hermes Armor is equipped. It temporarily enhances X's standard abilities, making him run faster, charge up faster, and fire five charged X-Buster shots at a time instead of three. It continually burns weapon energy when in use, and regenerates weapon energy when not. The more energy it has when used, the longer it lasts.
Giga Crash[edit]
This weapon is only available when the Icarus Armor is equipped. It unleashes a huge explosion that damages all enemies on the screen. A single use depletes all its weapon energy, but it slowly regenerates. It's still usable as long as it has any weapon energy at all, but the more energy it has, the more powerful the blast is.
Nova Strike[edit]
This weapon is only available when the Ultimate Armor is equipped. X dashes forward engulfed in a fiery aura, inflicting massive damage on any enemy he hits. It instantly brings any boss down to four hit points, but it can only be used in midair. A single use depletes all its weapon energy, but it regenerates fairly quickly.
Shouryuuken[edit]
This weapon is only available when the Ultimate Armor is equipped. Press 
+ Special Weapon when no weapon or the Nova Strike is equipped. X jumps up and performs an uppercut to damage enemies above him.