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The boots upgrade is found at the beginning of Web Spider's level in a cave hidden behind a waterfall. This gives you the ability to hover for a short time by pressing the Jump button while in midair. It also allows you to air-dash.
The helmet upgrade is found in Cyber Peacock's level. Get an S-rank in area 3 to get it. With this, special weapons won't consume any weapon energy unless they're charged.
Notably, there are actually two buster upgrades in this game. You can't equip both at the same time, so you have to pick one. However, you can always go back to the capsules to switch to the other one later. They are both found in Storm Owl's stage, above the spike-lined area. Use the Lightning Web to reach them.
The first capsule you'll find contains the Stock Charge upgrade. This enables X to charge up to four charged shots at once, and then fire them one after another. Note that the shots are not fired when you release the fire button; that just makes you stop charging. You must tap the fire button again to start firing them. This also enables X to charge special weapons.
Right behind the Stock Charge capsule is a second capsule containing the Plasma Shot upgrade. This gives X a bigger, much more powerful fully-charged shot that leaves behind a plasma ball on impact, which does further damage to any enemy that touches it. This also enables X to charge special weapons.
The armor upgrade is found in Magma Dragoon's level. You'll need the Twin Slasher and one of the buster upgrades to reach it. This enables X's Nova Strike Giga Attack, an extremely powerful air-dash attack. It needs full weapon energy to work, but it can recover energy either from weapon energy capsules or from damage X takes.
This armor can only be obtained with a cheat code. On the character select screen, highlight X, and press
twice,
six times, then hold
and
and press
. X will now be colored blue and purple when the game starts. Now, any upgrade capsule will grant X the Ultimate Armor. It's got the same capabilities as the normal armor upgrades (including the Plasma Shot buster upgrade), except it allows unlimited use of the Nova Strike, and you get it all at once instead of in pieces.
If playing as Zero, you can obtain his black armor through a cheat code. Highlight Zero on the character select screen, then hold
, press
six times, release
, hold
, and press
. However, all it does is turn Zero black, it doesn't enhance his abilities or anything.