Helmet Upgrade (radar)
- Stage: Crystal Snail
- Items needed: none
Towards the middle of the level, after you defeat the mini-boss and slide down the slippery crystal slope, there is a big chasm. Slide down the left wall of the chasm and there will be a path with some stationary enemies. Destroy them and keep going left until you find the capsule with the Helmet Upgrade.
This upgrade allows you to find hidden areas and passages elsewhere in the game when equipped. When using the radar you cannot use your X-Buster or any other weapon.
Leg Upgrade (mid-air dash)
- Stage: Overdrive Ostrich
- Items needed: Spin Wheel
This upgrade is at the end of the stage before you enter the door to the rocket. Before you drop down to the door do a dash jump across the gap to a ledge that is blocked by 8 blocks. Use the Spin Wheel to destroy the blocks in the way, inside is a small room with the capsule. Enter the capsule to gain the Leg Upgrade.
To use this upgrade jump then press the dash button to preform the mid-air dash.
Arm Upgrade (double charge shot)
- Stage: Wheel Gator
- Items needed: none; Leg Upgrade, Giga Crush or Strike Chain recommended.
Towards the beginning of the stage after you go down the two ladders, and before you jump down the hole to the rocket platform, climb up the wall on the right. There will be a small overhang to the left and another longer overhang a short distance to the left of the smaller one, in the middle is a vertical opening. Make X grab a hold of the smaller over hang using an air dash. Then let X slide off the small overhang and as soon as he lets go do another air dash to grab the longer overhang. You can also do this without the Leg Upgrade's air dash by doing a precise dash jump off the right wall, meaning you won't have to revisit here, but it is very challenging to do. The precise dash jump can, arguably, be made easier with the Strike Chain to help grip the wall. Climb to the top of the vertical opening and the capsule containing the Arm Upgrade should be on the right side of the room. One more way to do this is if you air dash after jumping off the right wall at the right time and then use the Giga Crush right after you pass under the smaller overhang. But you will need to be precise because the extra air from the Giga Crush won't lift you much.
This upgrade allows X to charge up and shoot two powerful shots from both arms. Like in the previous game, it also allows X to charge all of the other special weapons he gains.
Body Upgrade (Giga Crush)
- Stage: Morph Moth
- Items needed: Spin Wheel
In the beginning of the level, after reaching the giant ceiling magnets, throw a few Spin Wheels onto the ground after the second orange column. There's no crack or anything, so be sure to throw it after the second orange column; it's to the right of a large pile of decorative junk in the foreground. If you still have trouble finding it, use the Helmet Upgrade to help out. The Spin Wheel will break the floor revealing a secret passage leading to the capsule. If you have the Arm Upgrade, the charged Spin Wheel will break through the floor faster.
This body upgrade allows you to use the move Giga Crush, where after taking a certain amount of projectile damage (weapon energy bar must be full), X can unleash a powerful explosion attack that can deal massive damage to all enemies on screen. The attack doesn't work on bosses though. The upgrade also halves the amount of damage X takes as with the previous game.