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|Meta Crocomere||Pirate Undergrounds||Dodge the Crocomere's Phazon Clone beams, then fire your own Clone Beam at the beast's stomach. After a few rounds of firing, Crocomere summons a wave of lava. Use the Space Jump to jump over the wave, and repeat your attacks until Meta Crocomere sinks into the lava. Watch out for his claws!||Easy|
|Meta Kraid||Vehicle Storage||
Kraid attacks you in a sea of acid by clawing at the platform you stand on. Dodge five claws, and the acid rises, causing the platforms to rise. Go into a Morph Ball 2D section to reach a certain point on a long platform. Kraid grabs you and prepares to throw you into the acid. Quickly lay a Bomb into his hands. Four Bombs, and Kraid is defeated.
|Pirate Gunship||Laboratory||The Gunship circles you on a small platform. Take cover behind walls, and fire Super Missiles at the Gunship when it stops firing. After six hits, the Gunship starts sending troops. Defeat the troops, then shoot four more Super Missiles at the Gunship.||Medium|
|Hive Mecha II||Security Chamber||Fire the Clone Beam at Hive Mecha II, then roll into the Morph Ball to avoid the large hive of killer bees. After that, roll into the water in the stage and lay a Power Bomb in one of the three chambers. After that, you are knocked back on the orginal platform dodging hives. Repeat the cycle two times, and the Mecha shoots out fireballs as a core is revealed. Shoot at the core until the Mecha is defeated.||Medium|
|Draygon||Pumping Station||Start off by shooting a Charged Beam at Draygon, then dodge his ramming attack. After that, use a Grapple to bring down a pipe that keeps water in the chamber. Four pipes down, and the room is de-flooded. After that, Draygon is a sitting duck. Shoot him until he is defeated.||Medium|
|Mecha Ridley II||Chozo Ruins||Mecha Ridley begins to fly around the ruins, shooting missiles at Samus. You have to Grapple onto his chest and shoot him in the mouth until he shakes you off. He then lands, shooting plasma breath and slapping you with his wings. You have to wait until he flys again to begin hitting him again. At 25% health, his wings break, causing him to crash to the ground. He then begins to detonate explosives in the room until he is defeated.||
|Cloned Queen||Generator Room||If you know the way to kill the Queen, it can be easy. Lead it to the electrical wires, and it will become paralyzed The only problem is the Clone Metroids it spits out once paralyzed. Just freeze them, and Morph Ball into the Queen's stomach and let out a Power Bomb. Repeat the process unil she begins to spit out acid. You then have to fire missiles at the Queen until you defeat her.||Medium/Hard|
|Meta Brain||AI Chamber||
Meta Brain begins by shooting lasers at you. You have to shoot at the generators powering MB until both are destroyed. Afterwards, MB stops firing lasers, giving you a chance to shoot her eye. After a while, the generators are replaced.
At 50% of her health, MB releases waves of Phazon, damaging you if you touch it. At 25%, the room begins to flood with Phazon, with parts of the room still floating. Once you defeat MB, you have five minutes to escape the base, or it's an instant game over.