When you fight the 2nd form of Metroid Prime and step in his blue
Phazon puddles, enter Hyper Mode and attack with the Phazon Beam. No
other weapons will defeat him. However, he releases progressively
harder Metroids when he lays down Phazon, begining with Larva,
moving to Hunter, then Fission Metroids. Dispatch these much as you
would a Beam Pirate, with charged shots of the appropriate color. Do
not let them latch onto you.

The final Boss is difficult because of the Metroids it releases. You
can easily destroy them by entering the Phazon Puddle and blasting
them with the Hyper/Phazon Beam.

Use the following trick to kill Metroid Prime's 2nd form under
either the easy or hard difficulty setting. As you 1st enter the
battle, scan it immediately so you do not have to deal with it
later. The easiest way under the hard difficulty setting us to
always have the Ice Beam equipped no mater what the circumstance.
After Metroid Prime keeps doing the shockwaves and changes its
appearance, it will eventually send out a Phazon Pool. Jump into it
and blast Metroid Prime with all you have got. After awhile, it will
start making Phazon Pools and releasing no more than 2 Metroids.
Shoot the 2 Metroids with a charged shot, then shoot them with a
pair of missiles. Sometime after you do some damage to Metroid
Prime, it will then release 2 Hunter Metroids. Deal with them the
same way you did the normal Metroids. When Metroid Prime sends out
the Fusion Metroids, get into the Morph Ball and release a Power
Bomb to take them out.

Metroid Prime is an extremely difficult Boss. Before battling, have
at least have the Wavebuster, Ice Spreader, 150 or more missiles,
and all of the energy tanks. Having plenty of Power Bombs is also
recommended. Metroid Prime has 2 different phases. You will be
battling Metroid Prime through 4 subchambers in the 1st phase.
He will attack with a mouth-type-beam weapon, a grapple-beam-type
weapon that pulls you in (so he can hurt you by swiping his
forelegs), homing missiles, chemical missiles, an ice attack similar
to that used by Thardus, and energy orbs that deal massive damage
(but can quickly be disposed of by any beam attack). He will change
into random colors that make him vulnerable to the listed
beam weapon. When he is yellow, use your Power Beam and hit him with
2 Super Missiles. After you hurt him enough, he will turn black
and charge across the room. *** He will charge and change color at
any time in the fourth and final subchamber. When that happens, use
your Morph Ball and drop into one of the cracks in the ground. He
will not charge as far in the 1st subchamber; you will not have to
worry about using the Morph Ball. After he charges, he will change
into a different color. When he is purple, take the Wave Beam, get
fairly close to him, and use the Wavebuster until you hurt him
enough. When he is white, get your Ice Beam and shoot with one Ice
Spreader combo, then shoot at him with normal Ice Beam shots. When
he is red, take out the Plasma Beam and just keep shooting normal
shots while dodging his attacks. You can try to get close enough to
use the flamethrower if you have it, but he will strike you with his
forelegs. Metroid Prime's 2nd phase is much less complex than the
first. Lock on to him immediately. The only attack he uses is to
create a wave-like blast that just shoots out in a ring shape. The
1st time he uses that attack, all the pillars in the room will
fall apart. Use the Charge Beam to bring in any power-ups that came
out of them. Now, just release the charge. He is not vulnerable to
any conventional beam weapon. After a while, it will appear as if he
is releasing blue matter out of his tentacles. A pool of Phazon
forms directly under him, then Metroid Prime seems to have
disappeared. Remember where the pool of Phazon just appeared. Switch
to the X-Ray visor and lock on to him again. Try to step into the
small Phazon pool that he made. When you are in it, your gun will
automatically change to the Phazon Beam. The message "Hyper Mode"
will appear. Hold A and the beam will fire a continuous stream of
Phazon at Metroid Prime. The Phazon pool will eventually disappear,
and you will have to repeat the process. Whenever he disappears, he
always is visible through each visor in the same pattern: Combat,
X-Ray, Thermal, Combat, etc. Sometimes he may disappear without
leaving a Phazon pool. Later when he disappears, Metroid Prime will
also summon a pair of Metroids of any kind. It could be a pair of
normal Metroids, a pair of Hunter Metroids, or a pair of Fission
Metroids. When they appear, go into Morph Ball mode. Roll between
them and drop a Power Bomb. If done correctly, it should kill both
Metroids. If you run out of Power Bombs before you defeat Metroid
Prime, use an Ice Beam followed by a missile. This however, will not
help if they are Fission Metroids.

Use the following trick to kill Metroid Prime's Metroids faster. At
the battle between you and Metroid Prime's 2nd form, it sometimes
releases different types of Metroids when it makes the blue Phazon
pools. This makes it extremely difficult for Samus to shoot Metroid
Prime with her Phazon Beam as the Metroids will not let you shoot it
if they latch onto you. This trick works best on the Hunter and
Fission Metroids that Metroid Prime releases. When it makes the pool
of Phazon, get into the pool as quickly as you can. Now, shoot a
tiny amount at the Metroids that it released. They will blow up, and
you can get to Metroid Prime much easier because the Phazon Beam
kills them in one hit. Alternatively, use a Power Bomb and they will
also blow up. Make sure that you use the Power Bombs wisely. If
Metroid Prime does not make a pool of Phazon, no Metroids will
appear. This will save you a lot of health, especially in Hard Mode,
as the Metroids sap much more energy.

When you are fighting the 2nd form of Metroid Prime, it releases
different types of Metroids. The 1st types start at infant
Metroids, then Hunter Metroids, and finally Fission Metroids. When
Metroid Prime releases its 2nd little pool of Phazon, the
Metroids will appear. When this happens, get into the pool of Phazon
quickly. The Metroids will try to latch onto you. Before this
happens, shoot the Phazon Beam at them and they will blow up
instantaneously, so that you can shoot Metroid Prime faster. If the
Metroids do latch onto you, go into Morph Ball mode and lay a Power
Bomb (not a regular Bomb), because this will allow the other Metroid
to hit you and take your energy. This will save you a lot of health
and time.

First, blow away his Phazon armor. He will turn invisible and
probably unleash some troopers. Ignore them and use X-Ray vision to
find Omega Pirate. He is quite vulnerable when he is invisible. A
charged blast will take away a good amount of his energy. When he is
dead, he will melt and the Phazon suit will be yours.

The Omega Pirate is the 3rd to last Boss. First, find the 4
Phazon plates on the Omega Pirate's knees and shoulders. Shoot them
with Super Missiles or Charged Plasma shots. Once you break all 4
plates, the Omega Pirate will become invisible and send out
troopers. If you are lucky, you will get Ice or Plasma Troopers.
Destroy them quickly, switch to your X-ray Visor, then look around.
Most likely, the Omega Pirate will still be invisible, except for a
few Phazon-filled veins and heart. Avoid the attacks from him, and
in time he will uncloak. You will have to repeat the process.

When he charges up at a pool of Phazon, switch to Ice Beam and
charge. When it has completely charged, fire out using the Ice
Spreader (if available). This will cause more damage, saving you
health and time.

When fighting the Omega Pirate, do not use Beam combos while he is
in vulnerable form. In fact, when he is visible, his favorite weapon
is the Energy Siphon. This allows him to deflect missiles and use
your power against you from Beam weapons. However, if you shoot a
charged Plasma Beam Shot from Omega Pirate's right side (your left),
it will run into one of his legs. Now, the best place to shoot him
is from behind (this requires precision), as his armor is weaker
there. When he calls down the Power Troopers, look at what they are
located. If they are Plasma or Ice, take them down. Otherwise, kill
yourself; as you will never kill them in time. When you switch to
X-ray vision, find Omega Pirate and shoot 2 charged Plasmas at him
while locked on, followed by 2 single shots. He will disappear
again. When he reappears, shoot only one charged Plasma at him. If
he disappears twice while vulnerable, he will call down 4 Power
Trioopers. *** Before you fight him, scan him while he is in the
stasis tank, then run back to the save point. After saving, go back.
By doing this, when you die you will not have to fight the Plasma
Trooper again.
When you go in, he will jump out, When he does this, have your
Plasma Cannon ready and aim for a shoulder or a knee. Charge up and
when his hand is not glowing and shoot him. Two charged up shots
will destroy each shield. Make sure you have all your missiles. When
the other pirates show up, do a combo shot to kill them quickly. For
the white ones, charge up, freeze them, and fire a missile. Now,
switch to the X-ray visor, go to Plasma Cannon, and keep shooting.
He will then go to another place. With the X-ray visor on, shoot him
again. *** This will call more pirates back. Stay close enough to
him so that he does not fire his bombs at you, but not so close that
he stomps on you. When you back up against a wall, go into morph
ball mode then charge and shoot to the other side and repeat.

Look around the edge of the room and find a clump of rocks that you
can jump up and stand on. There is a nice one 2 sections to the
right of the door that you entered. From this vantage point, you
cannot be hit by the rolling Thardus or his ice attack that comes
across the floor. You can simply stay and continue to fire at him
with either the Wave Beam or your missiles. By repetitively shooting
your Power Beam at the rocks that he throws, you can continue to
generate power-ups which you can then tractor to you with the Charge
Beam. You can actually grow stronger with power-ups as you continue
the battle. You can continue this for the 1st several rounds of
the battle until the room is filled with fog. Now, run towards him
to target your missiles, as you will not be able to see him with
regular vision from your rock outpost. At this point you will have
adequate energy supplies remaining to simply stand and let him
pummel you with ice and by rolling over you while you target his
weak points with your Power Missiles. You will still be able to
retreat back to the safe area when it is time to return to using
your Wave Beam with your Thermal Vision. When you are not vulnerable
to his attacks, he is very easy to defeat.

When you enter the arena, go to the right. There should be a metal
beam close to the wall. Jump between the beam and the wall, and you
will be standing on a small platform where Thardus can no longer hit
you with his roll attack. Fight a normal battle with him until he
begins to form into a ball, Now, jump onto the platform again and
wait the attack out.

To defeat Thaardus, keep the Wave Beam on and get health as much as
possible. When he rolls into a ball, go into ball mode and power
boost away. Put on your Heat Visor and when he stands up, lock on
and shoot only Charge Beams. Watch out for when he roars and picks
up his arms. He will send ice on the ground toward you. Double jump
to avoid it. Also if you are in Heat Visor mode and he levitates the
rocks, lock on to them and blast them away. Be careful -- when you
break them, all you can see is yellow. Just quickly lock on and fire
repeatedly. When you are hitting the red spot with your Heat Visor
on, it will explode and your visor will lose power. Go back to the
Combat Visor and that spot will be blue, like the back of a
Sheegoth. Keep hitting it until it breaks and he screams. He will
roll into a ball. Just dodge it and repeat. After you drop his
health a few times, he will make the room foggy. Use your Heat
Visor. Watch out for the ice and rocks. You really cannot see them.
When you break his body plate (arm, leg, chest etc.), go into the
Combat Visor and you can see him. Repeat this until he dies. You get
the Spider Ball for defeating him.

Aqua Drone: Wavebeam or Wavebuster
Aqua Pirate: Charge Beam or Super Missile
Aqua Sac: Charge Beam, Wave, etc.
Auto Turret: Missile, Power Beam, Ice Beam
Baby Sheegoth: Plasma Beam or Missile
Barbed war wasp: Power Beam
Beetle: Any (best is Plasma Beam)
Blastcap: Any
Bloodflower: Plasma Beam
Burrower: Power Beam, Ice Beam
Chozo Ghost: Super Missile
Crystallite: Plasma Beam
Elite Pirate: Super Missile, Charge Beam
Eyon: Charge Beam
Fission Metroods: Any beam or combo Powerbomb, Phazon Beam
Flaahgra Tentacle (weakness is base of Flaahgra): Morph Ball Bomb
Flaahgra (weakness are mirror reflectors): Charge Beam Stuns
Flickerbat: Any
Flying Pirate (any combo): Charge Beam or Plasma Beam
Geemer: Any Beam weapon
Grizby: Missile
Hive Mecha (weakness are 4 red lights): Power Beam
Hive: Missile
Hunter Metroids: Ice Beam, Phazon Beam, Powerbomb
Ice Beetle: Plasma Beam
Ice Burrower: Power Beam, Ice Beam
Ice Shriekbat: Any
Incinerator Drone (weakness is red orb when in sight): Any
Jelzap: Combos
Lumigeck: Any Beam
Magmoor: Ice beam
Mega Turret: Wavebuster
Meta Ridley (weakness is chest and head): Plasma or Plasma Beam
combo
Metriod Prime 1 (weakness is face): Any Beam weapon
Metriod Prime 2 (weakness is head): Phazon Beam
Metriod: Ice Beam, Powerbomb, Phazon Beam
Oculus: Super Missile
Omega Pirate (weakness is Phazon Armor): Plasma Beam
Parasite Queen (weakness is mouth): Any
Parasite: Any
Phazon Elite: Plasma and Power Beam combos
Plasmatrooper: Plasma Beam
Plated Beetle (weakness is rear abdomen): Any
Plated Parasite: Morph Ball Bomb
Plated Puffer: Missile
Plazmite: Power Beam
Power Trooper: Power Beam
Puddle Spore: Any
Puffer: Any
Pulse Bombu: Wave Beam
Ram War Wasp: Power Beam
Reaper Vine: Any
Reaper: Any weapon
Sap sac: Charge Beam, Wave, etc.
Scarabs: Any
Scatter Bombu: Wave Beam
Seedling: Any
Sentry Drone: Wave Beam
Shadow pirate: Super Missile
Sheegoth (weakness is side of head): Missile, Plasma Beam
Shriekbat: Power Beam
Space Pirate: Power Beam
Stone Toad: Morph Ball Bomb
Tallon Crab: Any
Tangl Weed: Power Beam
Thardus (weakness varies): Charge Beam
Triclops: Morph Ball Bomb
Venom Weed: Any
War Wasp: Any
Wave Trooper: Wave beam
Zoomer: Any