Golem (Intro stage boss)

Aim at its head. Don't slash Ciel. When it fires the laser downward, climb the wall and hang out in the upper corner. When it fires the laser upward, stand just to the left of its fist, and the falling blocks shouldn't hit you. Once you get the Z-Saber, stand on the blocks or hang out on the wall until the Golem charges you, then swipe at its head. If you hit its head with the Z-Saber, you'll kill it instantly.

Ball and Mace ("Destroy Train" mini-boss)

Blast the pointy head with a charged shot or the Z-Saber (anything which does a decent amount of damage) to cause the robot to keel over, then attack the sphere at its base while it is vulnerable. You can also damage it while it is firing. If you attack the thing while it is shielded, you won't damage it, but you will push it backward slightly, which can be useful if it begins to get too close to you.

Engine Chamber ("Destroy Train" boss)

Avoid the fire on the front; after a few moments it will shoot nearly all the way across the screen, so you'll want to be standing on the far left to avoid taking damage. While the engine is shooting fire is when you want to make the most of every shot; charge up and fire only when the Joe isn't flashing. Once the engine is done using its fire attack, the parts of the floor will begin rising toward spikes on the ceiling. Try to move carefully so that you don't trap yourself (while still firing at the engine of course). It reacts to Lightning.Maha Ganeshariff ("Retrieve Data" boss)

Note: Once you win the battle, the place will self-destruct and you'll have to race it out. Start dashing and don't stop. The doors will all slam shut just as you reach them so be prepared to whack them to pieces with your Z-Saber or whatever weapon you have that is the most powerful. Also make sure you've taken care of all of your business in the underground lab before you start this mission, because you can't go back once it self-destructs.

Serpent Spider ("Occupy Factory" boss)

The machine's arms will generate various heads which attack you. Attack the gem in the center to damage it. You can only harm it when it's open (when the arms are attacking). What attacks the machine uses depends on what heads it's using at the time (the patterns are pretty obvious). You can destroy arms by attacking them while they are in head form, although they will be replaced in time. Also notice that the machine always follows you, so you can use this to lure it to where you want it.

Giant Mechaniloid (Save base event)

Keep following it and attack the missile in the back (it will flash when you hit it). Then shoot the part on the top to destroy the tank. You actually may want to wait a little while before finishing it off, because as the tank moves it will open up new passages that you couldn't access previously.

Air Statues (Neo Acadia Shrine mini-boss)

These twin purple flying suits (no BGC jokes please) don't have an energy meter so you can't tell how far you've whittled them down. Also they can't be frozen by the Thunder or Ice chips. They shouldn't be very difficult though; I'd stand still on one platform and just jump straight up over their shots (and them, if they're too low). Multi-Armed Statue (Neo Acadia Shrine sub-boss) This ugly-looking thing will throw its swords at you, and they boomerang, so be careful. You can avoid them effortlessly by staying on the wall until the swords return to it. It'll also act like a very deadly top (no Beyblade jokes please) but you can avoid this by being on a wall as well, or knock it out of it with a charged saber attack. This boss reacts to Lightning-that is, if it doesn't block your hit with its little shield.

Rainbow Devil (Neo Acadia Tower boss)

It's the Green Devil! Erm, sort of. It may resemble Mega Man's old adversary to a degree, but it doesn't fight anything like it. This is a nicely-animated boss who will leave you on your toes. When it bounces around the room you can cause it to split early by firing at the chunks, thus getting it to reform sooner and stop bouncing around. When it slides across the floor, do not stay on the wall over it, but instead jump over it and run across the room. Aim for the head, of course, to do damage.

Copy X 1st time (falcon armor form)

He seems to be able to use Master Weapons, interestingly enough. He moves around enough that it's hard to get him into a pattern, although generally everything he does gives you enough warning that you can dodge, as long as you're on your toes.Use charged shots when possible, of course. It may be that he's weak against various Elements based on what weapon he's using, although I haven't yet been able to verify this (typically, he switches weapons as fast as I switch Elements, so...).

Copy X 2nd time

There are certain constants in the universe. Like multiple final boss forms. And, in the finest X series tradition, the final boss is screen-sized while the first was humanoid. At least there's only one of him, though.

This one is tricky because of the pits and the fact that he's often not within your reach. Note that the fire he causes on the platform is his most damaging attack (not counting falling into the pit). You will want to learn the noise he makes right before he uses that fire laser, and immediately jump against one of the floating platforms and hang out there until the fire dies away. Do not stay on the floating platforms because the bands which bind you will throw you into the pit with no recourse if they catch you there. Note that the bands come down where you were standing as they were fired, so keep moving and you can dodge them. If you get caught, just press the buttons rapidly and you should escape before Copy X can attack you again. I believe Copy X is weak against Ice. The way I win this battle is using the Triple Rod, because when it's not charged, you can jump up underneath Copy X and fire it straight up and hit X almost regardless how high he is. Z-Saber slashes will hit him from underneath if Copy X is low enough, but I personally found the Triple Rod to be easiest. Note that the small yellow lasers Copy X fires generally will not hit you if you stand right under his head (which is what you have to hit to damage him, of course) so you can usually safely ignore those. Keep jumping and hitting him and dodging the fire and bands and you should have this battle won.

Naturally, if you die to the second form of Copy X and you have a Continue left, you have to start over with the first one (and all the plot as well).