Ahh... what would a Metroid game be without huge absolutely insane Boss battles? Simply put, it wouldn't be one. But entering the world of 3D changes the ground rules a little, perspectives have to be adjusted, bosses no longer have to fill a 2D screen, but a 3D screen. As such, in Prime, you have a better touch of realisim, when you realize that the Bosses you're looking at are nearly 10 meters tall or more.

Although the Queen of the Parasites is a sign of things to come in Metroid Prime, it is remarkably easy. Hit L to lock onto the queen and Strafe side-to-side, preferably in one direction, and shoot into the opening of the shield when you have a chance. Watch for the head of the Queen to draw back - this means she's about to spit a nasty goo stream. When you see Queeny's head draw back, quickly tap B while moving to one side to dash out of the way, and get ready to shoot missles and charge shots at her. Occasionally, the screen around the Queen will start spinning around, but it is still possible to hit the Queen by madly firing the Power Beam, but it's best to simply stop and charge up. Once the Queen is dead, escape from the Orbiting Frigate before it explodes. On the way you'll lose all your power ups and weapons, and run into an old... Friend.

This boss is fairly straight forward, and you'll probably take most of the damage in the fight from trying to scan the Boss. You may opt to not scan it, but doing so will ruin your chances for completing your Log book at the end of the game, as will happen with any boss.
Go to the center of the room and attempt to cross the bridge where the missle launcher is. The Hive Mecha will lock together and spit out 3 Ram War Wasps. First, look down towards where the bridge went under the toxic water with the scan visor and there should be your scan point for the Hive Mecha. As you scan the Ram War Wasps, as they fly around you will probably spin around with them as they fly about. Be on your guard as when they stop moving and hover, they are about to attack by Ramming you, hence their name, it is easy to step to the side as they ram and they'll likely miss.
With the Scan points out of the way, find the center of the main platform, stand there, and click down the R button so that you won't move from that position throughout the battle. Now, follow the War Wasps around as they circle around you and keenly look for the ones that stop. Pick them off with the Power beam as they do. After all 3 of the Wasps are destroyed, The Hive Mecha will have a glowing Red opening. Shoot the opening until it closes and the Mecha turns around for the next phase. This phase is the same as before, except this time there are 6 Wasps. After this phase, the same with 9 wasps. Once the Wasps are destroyed and you shoot the opening, the Mecha will split apart and let you have the Missle Launcher. Once the fancy cinematics are over, scan the blast shield on the door before blowing it off with a missle, and go in and collect an energy tank and a free energy recharge.

This Boss consists of two phases. The first is the hardest, as dozens of plain beetles pop out of the ground and come at you. Quickly tap the fire button to shoot the power beam faster and take out as many beetles as quickly as you can. Try not to use all your missles. Once the Beetles are dead, the second phase begins, and a Large Plated Beetle pops out of the ground and begins to "Dance" with you. Lock on with the L Button and keep an eye on the behaviour of the Plated Beetle and watch for it to lower the left side of it's head and squeal. When you see this, Dash quickly out of the way by moving to the side and tapping B. The Beetle will sail past you and it's tail will be vulnerable, shoot the tail with a missle. Power beam will also work but takes 5 times as long. Repeat this process until the tail explodes into a bubbling pile of goo. You may now collect the Morph Ball.
NOTE: Remember this tactic, this will also come in handy on other creatures, plus you haven't seen the last of the Plated Beetle. 

When you walk into the room, you'll see a Large Wasp nest on the ceiling and a Pole in the middle of the room. Scan the Pole. Now, move closer so it will engage. A rotating arm on the side will level out and shoot fire around the room as it rotates slowly. Lock on to the Pole and walk sideways around the room. After a few seconds, a red blast-point will pop out of the top of the Pole, shoot at it with Charged Power Beam shots or Missles. After the first hit, the Drone will fire straight up into the Wasps Nests. Get out the Scan Visor and scan the Barbed War Wasps that come out, these bugs won't be in the game again. In the Scanner information you'll find that these wasps can shoot stingers from as far away as 30 meters, so when  you see them, waste no time in destroying them with a few shots from the power beam. Try your best to avoid the flames from the Incinerator Drone as you deal with the wasps. There's no limit to how many Wasps there are so when the Blast Point pops out of the Drone, turn your attention to it and hit it with a Missle or Charged shot. Repeat this process a few more times until the Wasp Nest is incinerated. The Drone will then explode and reveal the Morph Ball Bomb.
Before leaving the area, there is a discoloured block on one side of the room, over top of one of the blue channels that runs through the floor. Blast it open with a Bomb to roll in the hole and get a Missle Expansion.

Flaahgra, when you first walk in, looks like a Giant Bloodflower. The moment you walk through the door the action begins, Flaahgra emerges from it's giant flowerbud and blocks the door off. Now's a good time to scan it.
Flaahgra has Channels in the surrounding moat around the Plant's base. Each channel is clogged up by a Tentacle. This is the closest point to you when the battle starts and is therefore the first place you should scan when entering the fray. Second, is Flaahgra itself, the scan point is on it's long neck up towards the head. Wait for Flaahgra to do a scare attack where it comes down and sort of stares you in the face, this way the Scan point is in range. Be careful of your position to minimize the potental for damage while trying to get a Scan lock. Once the Scan Data is completed, the Battle may commence.
Fighting Flaahgra may seem more difficult than it really is. To hurt it, you must first knock over the Sun dishes throughout the room that shine light on Flaahgra. Here's how you can make it easy. Lock onto Flaahgra and walk side-to-side and strafe around the entire circumfirence of the circular room. As you do so, Use charge beam shots or missles to daze Flaahgra, and while you do, the remaining Sundishes that are down, their blast-impact point will be right in front of you, back up or jump if needed and fire a missle, but do not release your target lock. Continue to daze Flaahgra as you proceed to the next dish. To speed up, rapidly tap the B button to dash around the Plant Boss. But remember to keep Flaahgra dazed or Flaahgra will knock any knocked over Sundishes back into position.
Once all the Dishes are out of position, Flaahgra will pass out, and the tentacles within the channels at it's base will retract. Roll quickly into the nearest channel, roll into the Ball slot at Flaahgra's base, and light off a Bomb. This is the only way to injure Flaahgra.
Once Flaahgra recovers, 2 Sundishes will fall instead of one. repeat the Process as listed above, Dazing the Plant and not letting go of your target lock. after 2 Dishes are done, 3 Will fall, then 4.
After the 4 Dishes have been knocked over and you move in to light off your fourth bomb, Flaahgra will die and you'll be treated to a nice spankin' new and very cool lookin' Varia Suit.

As you make your way into the Chapel of the Elders, you will find a bit of a Ball Puzzle. The door is blocked off by a Grate, with a bust of the Chozo Shaman at the corner. A quick scan will say something along the lines of "Seek my twin within this room". Go back to the entryway of where you just came in (no, not back down the shaft, it's on the same floor), you'll find 4 Busts on either wall of different Chozo people. The 2nd one on the Right Side, closest to the blocked door, is the Shaman. Blow off the head with a missle to reveal a Morph Ball Slot. Roll into the slot and detonate a bomb, and the grate covering the door will move.
Once you make your way through to the Chapel, you'll find that it's a large room with an Item sitting on the other side. The item is the Wave Beam. Once you reach it however, it will fall below the floor, and two of the corners of the room will open up and out will come two Baby Sheegoths. These Babys are easy. Use the Space Jump to Leap higher in the air to get a good shot with a Fully charged Power Beam at their back. One full charged shot will take the shell of their back. A few normal pelts after that and they're dead. Once on Baby dies, another corner will open and reveal another Baby Sheegoth. There are a total of 4 in this room, and will keep their numbers up to 2 attacking until there's none left. If you can, before finishing off the last Baby Sheegoth, try to go to the 4 corners where the Babies came out of. Crates of goodies are in those corners, blow them up and collect, and restore as much health and especially missles as possible. Once the last Baby dies, get ready for some action.
The Wall behind the Wave Beam will explode and out will come a rather peeved off Mommy Sheegoth. Handle this beast in a similar manner that you did with the Babies. DO NOT fire any Power Beams or Charge Shots at it, for they will only make the Sheegoth stronger, and increase it's firepower. Edge in closer to the mouth of the Sheegoth and try to get it to initiate a breath attack. Once it does it's Ice Breath or chucks giant snowballs at you, it will hyperventilate for a few seconds. Hit it with Missles, act fast enough and you'll get two missles in on it before it recovers. Repeat this process, run up to it's face and back off quickly, the Sheegoth acts in this Predictable manner. After a while of this, the Sheegoth will stop and let out a large groan. It is near death. Soon, the Sheegoth will flop to the floor dead and you'll be able to collect the wave beam.
(**= Charge Shots useful on Baby Sheegoths and ONLY on "Mommy" Sheegoth at very close range)

Once you enter the Quarantine Cave, you'll see a pile of rocks in the middle of the room. Switch to Scan visor. The Cinematics will begin shortly. Once they are over and the Rock Boss reveals itself, scan it to add the thing to your log book.
The key to killing Thardus is to locate a weak spot by switching to your new Thermal Visor and blowing the weak rock open with a Super Missle. Once the rock has been blown open, it will overload your Thermal Visor and you'll be able to see the weak rock and lock on using your ordinary Combat Visor. Another Super Missle will total it completely.
In the meantime, Thardus has 3 types of attacks, It summons up rocks from the ground and hurls them at you, it pounds the ground to do an Ice Quake that can freeze you, and it Forms a rather large ball and tries to crush you. Dealing with the first two is easy. The Rocks it hurls can be locked onto and shot out of the sky, the Ice Quake can be simply double jumped over or painlessly shattered out of (Rapidly tap B), but the Ball is the worst attack of the bunch which no doubt has sent many of Metroid Prime players GameCube controllers hurtleing to the floor.
Once Thardus rolls into a ball, you'll lose your target lock. The Trick to evading this attack is not to let go of your lock button from before it went into ball form and strafe straight to the side to get out of the way. Once it rolls past you, head straight forward for a few seconds, turn around and look for it. At this time it's just about ready to come out of the Ball, and it'll probably be nearby. This'll give you a few seconds to lock on, get closer and start attacking while Thardy gets ready for its own attacks. If you run out of Missles to hit it with Super Missles, switch to charged shots from the Wave Beam. They're not as effective, but hey, they're not Super Missles. :P
Thardus has about 6 rocks to destroy, Once you start attacking the rocks on it's head you know you're getting somewhere. It is also around this time that Thardus kicks up a Snowstorm that blinds the entire room with a white fog. There are two rocks on the head, and after destroying the last one, The last Rock will become vulnerable at it's chest. Hammer away at it and kill the beast, and collect your Spider Ball Prize.

After the fight, it may be instinctive to head back out from where you came in, but once you head back into the first room before the Ruined Courtyard, it'll be guarded by 2 Sentry Drones, and in the Courtyard itself, right before the save point, 2 or 3 Flying Pirates. Not a good route to take for a Samus who's currently weak and just got alot of work done that'd be bad to lose. Instead, in the Quarantine Cave there is a Spider Ball Track lining the Ceiling. Take your new toy for a spin and roll around to the back of the room on the top to a Previously inaccessable ledge. Behind the door is an elevator to Magmoor Caverns. Go to the Caverns and behind the base of that elevator, you'll find a safe and easily accessable Save Point. After that, go through the other door, out to the room called Magmoor Workstation, kill all the Flying Pirates and complete a puzzle to grab an extra energy tank.

It is my opinion that the Omega Pirate is, by far, the hardest boss in the Game. For this Boss, I recommend that you have alot of missles, alot of health, alot of luck and whatever God you believe in on your side.
The first thing to do upon entering the room, is switch to the scan visor and get a good look at the room. First you'll notice a large Stasis tank in the middle that holds a huge Elite Pirate, the Omega Pirate. Don't move in to close just yet, or it'll bust out of the tank and begin attacking. Next, you'll notice two patches of Phazon, one on either side of you, also note that there is another Phazon patch directly beneath the Phazon tank. These are key areas for later in the fight. Now, a look up at the Ceiling and you'll see a series of catwalk platforms at the top. In these platforms you'll see two rings, one ring directly above the entrance and one above the Sleeping Omega. Since when fighting Omega you'll be spending alot of time looking up at him, using the ceiling as a guide works pretty well at keeping mind on your location in the room, and therefore keep down the chances of getting caught between Omega and a wall.

When you feel ready to fight, get a scan lock on Omega's tank and slowly approach. Once your lock is successful, stop, and let the scanner finish entering Omega to your log book. Afterwards, switch to Power Beam and continue forward until the cinematics engage.

Omega Pirate is the peak of the Project Helix program and is heavily Phazon infused. It is invulnerable to attack so far as if at least 1 of it's 4 large Phazon crystals on it's body are intact. To hurt it you must first destroy the 4 Phazon crystals and force it into a Cloaked Regenration phase, where it will be briefly vulnerable to attack as it regenerates the Phazon Crystals over one of the 3 Phazon patches in the room, that you took note of earlier.
Omega also has 3 Major types of attacks that very much echo those of the other Elite Pirates. Wave Quakes, Hand Slashes, and Over-Shoulder Missles, as well as the annoying Energy Siphon.

Now here's how to crack the shell. Lock onto Omega and step back and side to side, slowly walking in circles around the Boss. Keep an eye out for the Catwalk Rings on the ceiling and use them as a guide so you won't be run up against the wall, this will keep you from getting way too close and reducing the risk of a giant and very painful hand slash. Keep a good distance, don't get too close (Hand Slash) and don't stray too far away (Shoulder Missles), stay within these ranges to best attack Omega, if you need to get around quickly, push hard to the side and use B to double dash around the beast. Charge your Power Beam, keep a good charge on and don't fire yet. Like the Elite Pirates, this will frustrate the Omega Pirate into pounding the ground with a Wave Quake. Here's your chance to strike. As the Wave Starts, jump in the air with your Beam still charged, and on your second jump, jump forward and Combo up the Super Missle. By doing this you'll jump over the Quake and on your way down, the Super Missle will impact on one of the Crystals before Omega has the chance to block the shot or absorb it with the Siphon. In the games Normal Mode, Omega usually only needs one direct Super Missle hit or 2-3 Plasma hits to bust a Crystal. Now, jump back and recharge your beam. Omega may do two or three Quakes in a row and that may make for the next Quake coming before you're charged up again, if so, just follow through and wait for the next Quake, jumping over it as it goes. Quake, Jump, Double Jump Forward and shoot the missle. Repeat this until Omega's Crystals have been destroyed.

When Omega loses the Crystals, it will now go into it's vulnerable cloaked state. As if fighting the huge behemoth wasn't enough, it will now call for the support of Power/Wave/Ice and Plasma Troopers for aide in taking you down. If you have alot of heatlh (and even if you don't), for the most part, jump around alot to avoid getting hit by their blasts. Identify what types of troopers they are and attack them with the Beam required. Power Troopers need only one Super Missle hit, Ice Troopers need only a charged Ice blast to freeze followed by a shattering missle, Plasma about 2 charged hits from the Plasma beam. If they're Wave Troopers, they will take too long to take down, so ignore them but be mindful to where they are. After about 5-10 seconds since Omega cloaked, Switch to X-Ray and Power Beam, charge up and search each of the 3 Phazon patches with a quick glance for Omega to appear(jumping while you do so to avoid any remaining Trooper fire). Once you spot Omega, lock onto it's heart and let a Super Missle rip, Charge up and fire again if you can. If it winces in pain and dissapears again, charge search the Phazon patches again for it to appear, it will be vulnerable to attack for a few short seconds before it's Crystals are restored. Under the games Normal Mode, It 'IS' possible to bring Omega down to less than half of it's health before it's back up and running.

Once Omega's back on it's feet, resume the Crystal bashing Super Missle attack and dodge the shots from any remaining Troopers. Getting in a little closer (but not too close) may trigger more Wave Quake attacks, these you can use to your advantage because it will not only give you a good chance to attack, but also eliminate remaining Troopers - which alot of the time will leave some rather juicy powerups.

As Omega cloaks again, examine what type of Troopers come out to play. This time there may be more than one type and more Troopers than before. With Omega closer to death, just try as best you can to stay clear of their blasts and deal with the quickly dealt with Troopers. Once Omega appears in XRay, nail the heart with Super Missles and prepare to attack Omega again. Don't worry too much about the Small fry Troopers, with Omega near death, once Omega is destroyed, the remaining Troopers (in both Normal and Hard modes) will simply disappear.

When the last shot is fired, Omega will crumple to the floor - right on top of Samus. When the bubbling of Omega turning to Pure Phazon occurs, Samus will pop out wearing a VERY slick looking Black & Red Suit, that has been infused with Phazon and prevents future damage from Blue Phazon deposits. It won't help against the Orange Phazon in the Impact crater, however.

After the battle, head to a lift on the right side of the room and activate the panel, go up to the Catwalks, find the door and collect the Energy tank right on the other side of it. Turn back and head for the door you first came in and go to the Save Station. Be warned that because all Space Pirates in that room have been killed, the room is now filled with regular Metroids. Eliminate them however you see fit and Save your game at the Save Station. Head back into the Mines and look for the Morph ball only room called "Phazon Mining Tunnel" and down to the lower level infested with Phazon, where you couldn't tread before. The Artifact of Newborn resides at the end of the Trail.

Once you've collected all the artifacts you'll be treated to a wonderfully mystical scene as the artifact stones activate the gateway in the Middle of the Artifact Site. Too bad it's not that easy. As soon as the Central porthole opens up, Ridley will fly by and destroy the Center stone and begin attacking you. Before the cinematics end, you'll be hit by bombs, don't worry, it's just cinematics, they don't hurt you. But be careful because the next ones will. Now's a good time to try and scan Meta-Ridley for your log book,  Switch to Plasma beam and begin charging. If you have to use Super Missles to quicken the pace, do so, but Charged Plasma shots do nearly the same amount of damage. It is my strong suggestion that you use little or no missles in this phase of the battle, for the less missles you use can make this a short fight later.
Ridley will do 3 different types of attacks in his first phase. One, he will hover just off the outermost edge of the Artifact site's bowl. This is where you can do most of the damage. Pump his chest full of Plasma. Each successful hit will cause Ridley to lurch back and squeal. On occasion Ridley will cover his chest with his wings, get ready to fire a blast once his wings open, and double jump forward to avoid the barrage of missles he was preparing to fire.
The Second attack, Ridley swoops by spitting Laser and dropping bombs. To best avoid this attack, get to the outermost edge of the bowl and Jump over the Laser, and use your second jump to avoid the bombs. Using this tactic, you can usually get though relatively pain free. Note that Ridley flies too fast for a good hit from a Plasma bolt or a Super Missle.
The Third attack is the hardest to deal with because Ridley lands on the ground right in front of you, and will try to turn around looking for you, and in the process swat you with his tail, or swipe you with his claws. During this time back away and continue to pelt his Chest with Plasma, Sparks fly out and Ridley won't react to the damage but it will signifigantly hurt him.
Continue this attack process until Ridley's health drops to about 25% and his wings begin to catch on fire and burn up. Once you see fire on his Wings, it's not the Plasma beam's burning effect, switch immediately to Wave beam.
The Next Phase is the toughest, as Ridley lands on the ground and begins to fight Melee style. If you were to handle this attack to Beams and Missle attacks, what you would do is watch for Ridley to open his mouth and fire a charge shot or missle into it. Doing this will make Ridley reel back in pain and expose his chest, leaving a clear shot for a Super Missle or an Ice Spreader. But be very careful as the danger of this attack is high. Miss the mouth and Ridley will close it and most likely Ram you afterwards, which will hit you for nearly half a tank of energy. As well as a Tail swat for more damage as you run away. Plus, if the hit is successful, you might miss his chest as Ridley recovers.

This battle will prove to all just how much you've learned in this game. This entire process will call on all the knowledge you've learned to this point, the more you know, the better off you are. Getting to the site where Metroid Prime is located is tricky by itself, as you have to scale an entire room full of platforms all the while avoiding the Fission Metroids that will try to get in your way. But first, scan the Lumigek's that swarm the wall as you make your way deeper inside. As you head up through the main chamber, head directly and quickly to the other side towards the white teeth on the wall. Afterwards there is a series of floating platforms to jump on, if at any time you see a Fission Metroid fly past you or graze you, immediately get secured onto a platform, roll into a Ball and light off a Power Bomb, this will elinimate all nearby Metroids. On the side halfway to the top there is a Missle station, if you need missles, use it. if you don't, keep trudging along. You'll probably run into a Fission Metroid waiting around the corner, power bomb it. Keep jumping up floating platforms, if you don't see the next one it might be behind you. Make your way quickly to the door at the top. Try to save at least 3 Power Bombs for the final fight scene.
Once you make your way into the Cavern that contains Metroid Prime, the Cinematics begin. Prime sees you and runs away. Get out the scan visor and give chase. In the next room, Prime turns to fight, get closer to scan it.

Now for Battle Schematics for Metroid Prime. Because Prime assimilated some Space Pirate technology, including some of the work they were doing with adapting your weapon technology, Prime has developed an enormous Exoskeleton and many different attacks. The first thing you must do is identify the markings on Primes face, the little circle like spots below the eyes, and the circles around the front leg joints. There are, like the Troopers, 4 different colours which can be matched with beams.
Yellow - Power
Purple - Wave
White - Ice
Red - Plasma
Dealing with each beam type has different methods for you to attack. First of all, the only way to hurt Prime is by shooting the red eyes with the Beam that corresponds to the Facial markings. With the the Power Beam, use Super Missles. Ice Beam, Ice Spreader. Wave and Plasma both with charged beam shots, although short bursts of the Wavebuster are effective.
When to shoot, however, is tricky. Although Wave beam and Super Missles usually home in on the target, Ice fires slowly, a Super Missle might bounce off the Exoskeleton and Plasma shots are ineffective when Prime's face is in different positions. When the face is pointed up and is shooting a Beam, the best time to shoot is the very top of your double jump. By the time the blast reaches Prime it's head will be on the way down or tilted low enough for a direct hit. With the Wavebuster, be careful not to drain your missle supply as many of these attacks require missles and are much more effective than the Wavebuster.

Here, Prime also has 4 phases in which it attacks you, dependant upon how much damage you've done to it.
First Phase:
Attack Prime enough to make it reel back in pain 2 times. In this Phase it's primary attacks are a large powerful beam shot from the underside, and a volley of missles fired from the back of the beast. The Beam doesn't move after it's been shot, so just double jump around it. If it's an Ice Beam, just jump rapidly to get free like you did with the Sheegoths and Thardus. The Missles can be avoided by dashing forward. After Prime's been hurt once, it will lunge at you, so back off behind the objects sticking out of the ground.

Prime will hightail it underground to the next location.
Second Phase:
Make Prime reel back in pain 3 times. A new attack appears in this phase where two balls of energy will shoot from primes back and slowly make their way to you. IMMEDIATELY target these two and shoot them down with plain missles, one for each ball. If they get too close they'll get harder to hit and they do severe damage upon impact, and taking them out usually leaves behind some juicy powerups, mainly Ultra Energy and Missles.
When Prime is hurt, DON'T THINK about it, just get into a morph ball and boost-roll into one of the side grooves in the floor and not the middle. Prime is about to charge over to the other side of the room and it's rear leg will land in the center groove. Keep attacking

Prime will head underground for the...
Third Phase:
Hurt Prime 4 times. A new attack appears where Prime will latch a Tractor beam onto you an drag you forward. You can use a Power Bomb to break loose, but that wastes your remaining power bombs you'll need for later. The best way to get free is to slip into a Morph ball and boost backwards. Attack Prime normally.

The next phase is the hardest of them all.
Fourth Phase:
Prime must be hurt an indeterminite amount of times, based on how much health it has left. Prime will now begin attacking franticly and switching beam-types randomly, faking attacks, and charging at you at will without being hurt. So cut loose with the Missle combo attacks and use whatever you can, because you'll only need a handful of Missles left(10 or so) afterwards. However, The Flamethrower is still a waste. Stay on the ball and keep with the Beam-type changes and drag Prime down however you can.

Once it's health is diminished, it will stumble through the floor and land in the next room, Prime's Lair.

When you land you'll see the Exoskeleton melting into a bubbling pile of Phazon. Then Prime itself will emerge! A 6 Tentacled freak of a Metroid with a 3 Hemisphered brain and a spooky looking face. A quick scan will reveal that it can't be hurt by Beam weaponry(plus, if you scanned everything in the game - right here is where you'll find out if you got 100%). It's time for some Phazon beam action. But how do you use the Phazon beam anyway? Wait and learn. Prime will attack mainly with a Flame Quake, and an occasional "in your face!" move with is merely intimidation. Just double jump the Quakes and keep a lock on Prime. After Primes very first Quake, the Objects sticking out from the ground will be destroyed, leaving behind some Ultra Energy balls and Missles. Collect what you can between Quakes. When Primes Tentacles point straight at the ground, a Pool of Phazon will form, and Prime will disappear.

But Prime didn't really disappear, it has just become visible only to another visor. In fact, Prime's phasing in and out of visibility actually occurs in a very predictable pattern.
Combat Visor -> X-Ray Visor -> Thermal Visor -> And back again.
By using this information you can now take out Prime with the greatest of ease. Walk over to and stand in the Pool of Phazon Prime has left behind, this will activate the Phazon Beam. Locate Prime and lock on, and unleash hell. Continue this, rotating the visors as it phases out of sight. If you lose track, just simply look for the center where the Quakes are coming from and then check the other two visors.

As Prime's health fails, it will Spawn other Metroids for help when it creates a Phazon pool. What type of Metroids depends on what Primes health is at, and there's always 2 at a time.
Below 60%aprox - Normal Metroids
Below 40%aprox - Hunter Metroids
Below 25%aprox - Fission Metroids

Normal and Hunter Metroids are easily dealt with. Use the Ice Beam to freeze them and shatter them with Missles. Fission Metroids are trickier but not too tough, get into a ball and roll directly between them as they stop to charge with an attack. Set off a Power bomb and listen for the 2 *pops* as the Metroids go bye bye. Remember, thw quicker you get the Phazon pool, the more of the pool you can use, and the faster you kill Prime.

However, be it Hard Mode or Normal Mode, this phase of Prime is always simple, just keeping in mind that Prime has a Predictable order for Visors, and dealing quickly with the Spawned Metroids, with secure you the ending sequence you deserve. :)