As in the official games, X acquires new weapons by defeating one of the main 8 bosses. These weapons consume ammunition, which can be refilled via save capsules or from blue item pickups in the field. Unlike in the official games, these "special weapons" do not require an arm upgrade to charge; instead, their charged variants are unlocked via spending points on the requisite section of their independent skill trees.

Missile_barrage.png|thumb|link=#Missile Barrage| Missile Barrage File (2).png|thumb|link=#Stun Spark| Stun Spark Plasma-2.png|thumb|link=#Plasma Bouncer| Plasma Bouncer Crystal-0.png|thumb|link=#Crystal Bomb| Crystal Bomb </gallery>

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  Force Breaker

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  Warp Vortex

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  Cyclone Razor

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  Swarm Barrier

Missile Barrage

Missile Barrage
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Missile Barrage is one of X's special weapons, received from defeating Warfare Milodon. X aims upward and launches a series of missiles that travel up to the top of screen, ignoring all walls and surfaces. They then return falling downward from random positions and homing in on nearby enemies. This weapon can be fired in quick succession to launch multiple missiles.

Stun Spark

Stun Spark is one of X's special weapons, received from defeating Sparking Scorpio. This weapon creates an electrical field around X that fires lightning bolts horizontally, or vertically if the up button is held. These bolts do little damage, but stun enemies, stopping them from moving (causing flying enemies to fall), as well as preventing them from inflicting contact damage.

Formerly, this weapon released an electric orb that dropped to the ground and travels along the ground, or could be aimed up to the ceiling instead. When the button was pressed again or the maximum distance is reached, the orb expanded into a large stationary field that persists for a short time, and launches a bolt of lightning opposite from the surface the field detonates on.

Plasma Bouncer

Plasma Bouncer is one of X's special weapons, received from defeating Plasma Puffer. X fires two bubbles up and down diagonally which can bounce off of surfaces. This weapon is unique in that it only uses half a point of weapon energy per shot.

Crystal Bomb

Crystal Bomb is one of X's special weapons, received from defeating Crystal Rafflar. X fires an arcing projectile that can be aimed up or down, which then creates a temporary crystal growth when it touches a surface. If the bomb impacts a strong enemy, it will break into shards that arc off from the enemy and produce smaller crystals where they land. All parts of this weapon are able to reflect enemy energy attacks back at them.

Force Breaker

Force Breaker is one of X's special weapons, received from defeating Force Starfish. X fires a blast of energy that dissipates into a circular explosion after a short distance, dealing damage-per-frame (like Zero's saber attacks) instead of a single hit on impact. This weapon is able to damage and destroy armored enemies and crystal blocks.

Additionally, this weapon can be fired downward in the air, which grants X a small height boost and maintains his momentum.

Warp Vortex

Warp Vortex is one of X's special weapons, received from defeating Warp Vulpex. X shoots two black holes that spiral around each other. They absorb enemy projectiles, but this weapon is probably getting reworked to be cooler.

Cyclone Razor

Cyclone Razor is one of X's special weapons, received from defeating Hurricane Hoatzin. X fires a spinning blade of wind energy that travels forward a short distance before arcing upward and dissipating. The blade is able to pass through walls, as well as enemy shielding allowing it to damage their unprotected side. Additionally, this weapon is able to lift mobile enemies off the ground and carry them a short distance, and X can jump into it to gain a height boost as well.

Swarm Barrier

Swarm Barrier is one of X's special weapons, received from defeating Neurohack Mosquito. It is currently undergoing a rework, so remind Keiang to update this section once that's been finalized. It used to be called Neurospike and would let you force enemies to act as your allies, but it wasn't very effective, as cool as it was, so it was scrapped.