After you make your way through the traps, puzzles, and battles in Bowser's Keep, you confront Magikoopa.
Magikoopa is weak to normal attacks, so use those throughout the battle. Magikoopa can use Water Blast and Solidify, which hit all characters. Magikoopa can cast Willy Wisp, Bolt, and Blast, which hit a single character. Magikoopa can summon monsters to hide behind. Defeat the monster, then resume attacks on Magikoopa. Bahamutt can use Iron Maiden to inflict Fear status, and can throw a boulder at a character, doing high damage. Bahamutt is weak to Ice. Jinx Clone is weak to Special attacks. Jinx Clone can cast Jinx, Triple Kick, and Quicksilver, which each hit a single character. King Bomb is weak to Jump and Fire. If you don't defeat King Bomb in time, it casts Big Bang, doing high damage to all characters.
After the battle, Magikoopa creates a treasure chest that will never run out of coins. You can talk to Magikoopa to fill your HP and FP.
Go into the northwest room to find Croco, who is selling some new armor and the same healing items as before. If you can't afford something, you can always go to Magikoopa's coin chest and hit it until you have enough.
When you're ready to continue, go through the east door.
Carefully go northeast, but beware of the Thwomps up ahead. They will stop you in your tracks for a moment, and you might get hit by a Big Bertha, which you will have to battle. You can also jump on top of a Thwomp to go to the upper level, but there is no treasure up there, and Big Berthas can still hit you on the upper level. When you get past the enemies, go through the northeast door.
Go northeast through this hallway, and there will be a cutscene. Then you will battle Boomer.