Arachnus/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 its 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!
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.
Pogo/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.
Serris/Speed Boost Guardian
This boss is Serris, who was infected and killed by an X parasite who took over its form. One of the more dangerous bosses, it moves quickly and inflicts great damage. Shoot its head with a missile or charged beam, then quick;y jump out of the way. When the boss is flashing, he moves considerably 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 ladders to the left and right and on the ceiling are useful to dodge attacks. You can avoid virtually all of Serris' attacks by staying at the very top of the right ladder to make an easy (and boring!) fight.
The Core-X is better fought on land than 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. Hang onto the ceiling, and wait for it to come under you, then shoot. Its 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, and is sorrounded by a ring of tiny versions of itself. These can be destroyed but you should concentrate on the central Core-X. 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. The Core-X swings about the environment on curved swoops, and since it is so large and fast, it can be difficult to avoid damage. Keep your beam constantly charged and somersault jump when avoiding it when possible. That way, if you are unable to jump out of the way quickly enough, you will still inflict a hit with your mock Screw-Attack. After it changes color, hit it 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.
Arachni-X/Space Jump Guardian
The Arachni-X is probably the most difficult boss in the game. The battle is fought in a very tall, relatively thin silo, and Samus has the run of the floor while the large Arachni quickly scuttles above her. Samus must repeatedly fire missiles into the creature's open mouth in order to defeat it.
The Arachni-X makes his entrance shortly after yours - a distant explosion, followed by three clumps of fire which burn for a short period of time in the far corners and one in the middle of the floor. Arachni-X will 'bounce' around above you in a logical but unfixed pattern. Occasionally he will stop and open his maw for a few moments in order to spit more clumps of fire out. It is at these points that Samus must quickly fire as many missiles as possible in order to damage him.
Aside from these times, he is invulnerable. Your biggest worry is avoiding him. If gets relatively above you, he will seize Samus and slowly pull her up to the top of the silo before slamming her down. As he pulls Samus up, he will sap her health and the poisons make it difficult for Samus to resist. Rapidly button bash as he draws her up to reduce the time he has a grip on you. Either way, Samus will take substantial damage from this attack. The impact also causes Samus to bounce from the ground as she slams into it, and you must be quick in getting out of the way after this happens, as he can very easily pick her up again!
Morphing into a ball will help you avoid this. However, be aware that the fire Arachni-X spits out causes Samus to bounce up when in contact, sometimes pushing her right into Arachni-X's pincers. Also the fire reduces the area in which you can run briefly; jumping is dangerous, again as you can cause Samus to leap right into his mouth.
After you have fired enough missiles (Arachni-X will change colour and will become faster) his legs will drop off and he will somersault at ultra-high speeds in succession in order to 'fly' above you, spitting chunks of mass in order to damage Samus. His mouth, however, is permanantly open. Standing in a corner and shooting constantly will often be enough to damage him and destroy any of his incoming attacks. He will then turn into the usual Core-X.