New Game+: v4.0 adds one to the game along with the save function, allowing you to take every upgrade along, including the MAX Hyper Armor/Black Armor.
Lightning Bruiser: The v4.0 makes the Black Armor turn Zero into this, increasing jump height, dash speed and length and his walking speed, while also increasing his defenses and damage output.
Double Jump: Zero can get this ability from the Leg Upgrade Capsule in Blizzard Buffalo's stage.
Volt Catfish's Mercy Invincibility is changed on v4.0 due to his ridiculous frames, in exchange for now being frantic.
Also, some blockades which originally demanded charged weapons to work were changed to accomodate for Zero's limitations. Zero becomes a slower character and loses the ability to charge special weapons, but comes with his Double Jump and Air Dash in hand, and his Black Armor basically makes him frighteningly agile. To make up for this, Zero has a larger hitbox, gets no defensive upgrades (barring the Black Zero Armor, and uses more weapon energy.
Competitive Balance: Zero starts out with a double charge shot and the ability to charge special weapons, while X has to find armor parts to do these.
The updated inventory in v4.0 allows you to keep track of both Zero and X's life gauges at the same time.
Not only that, it also saves the MAX Hyper Armor/Black Armor upgrades and you can carry them over to the New Game+ along with Zero's saber.
The new save feature also saves your Subtank load, saving you the trouble of stopping at a completed stage to fill them.
Its properties are also changed instead of spreading out when they collide, the Cross Buster now crosses itself at a point, allowing you to hit things with all pellets if you get the range right.
The X-Buster upgrade works like the upgrade from Mega Man X2 by letting X fire both charged shots at once rather than stopping him in place to prepare the next shot.
If the Mosquitus miniboss in the second Doppler stage is beaten as Zero, however, he will still be rendered unplayable for the remainder of the game.
The hack removes the original game's Character Select Forcing by letting Zero face bosses and minibosses rather than forcing him out of the stage with X.
Zero also gets his own dialogues and ending to keep up with X.
Should you choose to, when he's captured by Mac, X takes his place in that section of the stage and Zero even berates himself for falling for Mac's trap.
In v4.0, Zero is also playable right from the intro stage if you want.
In v4.0, he loses the capability of charging special weapons and using upgrades in exchange for being able to Double Jump and air dash on the fly and his Black Armor gives him a massive agility upgrade.
Adaptation Expansion: Zero can now use weapons, and Ride Armors.