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First Things First
When I first played Metroid Prime 2 on the Gamecube, I was surprised at how much more difficult the bosses were than the ones present in Metroid Prime 1. For the sake of newer gamers, Nintendo has lowered the difficulty of the normal mode, so if you want an experience akin to the original version, you'll want to start a file on hard mode.
Of course, since this is still Metroid Prime, you'll want to scan everything. Most of the bosses in Metroid Prime 2 have multiple forms or phases, which means you'll be switching to the scan visor often to log new forms and reveal new weaknesses.
During most of the boss fights you'll have safe zones in which to replenish your energy at a slow rate, but any dark projectile attacks can disable the light crystals temporarily, so beware!
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Dark Alpha Splinter
Your first boss battle is an Ing possessed insect that won't give you too much trouble. Its only methods of attack are a spit and a charge, neither of which are too difficult to avoid. The Dark Alpha Splinter tends to charge just after spitting. Just strafe around the boss and keep your distance from it, plugging charged power beam shots and missiles into it whenever you're not dodging an attack.
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A slightly more dangerous foe than your last boss encounter, the Bomb Guardian has several modes of attack. As it slithers its way around the room, the guardian will drop bombs to try to prevent you from following it. Occasionally, the front end of the worm will spit out a handful of spreading bombs, or a single homing bomb.
The objective of this fight is to fire at the tail until it stops dropping bombs, at which point it will raise its head to fire an energy blast at you. Strafe around to its front side to blast it with a charged up power beam to score some real damage. It will take a few rounds of disabling the tail and firing at the head to destroy the guardian and get your bombs back.
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You'll find yourself dodging for a good portion of the fight against this Space Jump enhanced Ing. The creature will keep a barrier up around itself before it makes a leap, and that barrier is turned into a shockwave when it lands. Keep an eye on your radar when it leaps out of sight, and time your jumps carefully to keep from being knocked out of light filled bubble. Apart from the shockwaves, the Jump Guardian will slash at you when you get too close, and will generate thin beams of energy that fire very quickly.
The boss will rarely step into the light to attack you, and the beams will come out at regular, easily anticipated intervals. Your best chances to attack are just after it lands, and when it's firing beams at you. The less life it has left, the more it tends to jump.
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Dark Samus (First Encounter)
Dark Samus darts around the room, giving you no chance to use charged shots or missiles. Her single shots are easy enough to avoid, and whatever you do don't get too close to her. Just stick to simple power beam shots, and use the objects in the room to stop any major projectile attacks she throws at you. Keep in mind, however, that if Dark Samus destroys one of the pillars in the room, the fire from the wreckage will hurt you.
Dark Samus is quick, but she announces all of her attacks with visual cues. If she lifts up off of the ground, then you'll have a missile or two to dodge. If she begins to charge up energy, then she'll unleash a spray of Phazon energy. In both cases, you're better off finding shelter.
At half health, Dark Samus will absorb some of the Phazon in the room and take on a continuous glow. Now, if she drops to the floor and charges up, she'll launch herself at you in a pretty devastating attack. Keep up a relentless barrage of power beam shots, and you'll send her running soon enough.
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The fight begins with something burrowing underneath you, and a large black orb sitting in the middle of the area. As the scan reveals that the orb is invulnerable to weapons fire, your target is the worm -or worms- under the earth. Watch the radar and keep away from your foe as it leaps out of and back into the ground, and fire light beams or missiles at it as it sails through the air.
As you damage the big ol' worm, you'll be able to see the effect you're having on its shell. When the worm's armor is gone, it'll attach itself to the orb and begin to fire dark energy at you. Keep pelting it with your weaponry until it loses a second set or armor and falls to the ground. At this point, the worm will start to inhale; contrary to the logic of self preservation, you'll want to roll up into a ball and let it suck you up. And if you haven't guessed by now, the reason for offering yourself as a snack is to drop a bomb inside of the beast. The worm, in its agony, will lift up the black orb and slam it into the ground, cracking it.
And now it gets tougher. A second worm will join the fight, and you'll have to get both to attach themselves to the orb, and drop bombs inside both of them to get them to damage the orb further. And once that's done, you'll have to do this one more time, with -you guessed it- three worms. The energy projectiles will increase in frequency as the fight progresses, and when three heads are present, they'll fire beams of energy that will roam around the area for a while before ceasing. With the attack over, shoot and bomb your way to victory and a new suit.