Morph Ball Guardian
As soon as it takes its form, pump missiles into its belly. If it scratches the air twice, be warned, because it's about to shoot a wave of energy at you, which does moderate damage. If it screams, jump onto a ledge nearby to dodge the fire. Once it's in it's ball mode, you can hurt it, so use a ledge to jump over it from high above. If it hits the wall you're clinging to, you'll fall and take damage. Simply repeat the process to make it transform back into a Core-X.
This part is fairly easy. If you ran out of missiles, grab the green X floating around, then hit the Core-X with a missile whenever it isn't flashing. Dodging it shouldn't be hard. Three missiles will finish it off easy, and now you have the morph ball!
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Charge Beam Guardian
This fight is really just practice for the tougher Core-X form. All you have to do is keep from getting hit. When it is charging up to fire, it will open an "eye" - shoot it with a missile then jump away immediately to avoid the blast. A few hits will do it. Once it's dead, grab the giant X for the charge beam ability.
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High Jump Guardian
To defeat this boss, you will need to dodge it until it opens its mouth and floats down slowly. Then, shoot as many missiles as you can into it, and run away. If you get stuck, bomb your way out. The Core-X is almost the same as with the Morph Ball Guardian, just a bit stronger and tougher.
Speed Boost Guardian
This boos is Serris...who was infected and killed by an X parasite who took over its form. Shoot its head with a missile, then jump out of the way. When the boss is flashing, he moves faster than usual and is invincible to attacks. It may be hard to hit him, but watch his actions, dodge, and when you see him come at you, unload. The Core-X is better fought on land then underwater, since you can move more quickly up there.
B.O.X. Security Robot
Unfortunately, this boss will not give you any power-ups, since it's not X-infected. Or maybe that is a good thing. Who knows...but anyway, you will need to fight it to clear it out of your way. Hang onto the ceiling, and wait for it to come under you, then shoot. It's attacks include jumping at you and releasing a ball that opens a pillar of fire in both directions. When it lowers, move to the other side, since it comes back up before disappearing. Around 10-12 hits will make the robot go off to the side and create a passageway for you to follow.
Varia Suit Guardian
The Core-X who stole the Varia Suit became much bigger. Missiles are useless here, so charge your beam and wait for it to go in your firing range. Make sure not to fall into the water, since that slows you down tremendously. After it changes color, hit is a few more times, and defeat the Core-X to claim what you deserve.
Wide Beam Guardian
He may look like a scientist, but don't be fooled. This is another Core-X, similar to the one fought when getting the Charge Beam. To get it to change, though, shoot a few missiles at it. Remember you have limited time, so hurry up. After retrieving the Wide Beam, step onto the controls to cool down the heating unit and stop destruction.