This is a list of bosses and how to defeat them in Super Mario 99 from first to last.
Big Bob-omb is the boss of Bob-omb Battlefield. The massive Bob-omb will try to pound you and throw Bob-ombs at you too. To damage him, you must pick up a Bob-omb and throw it back at Bi Bob-omb, similar to the Big Bob-omb boss fight in Super Mario 64. After hitting him with three Bob-ombs, he'll say "Enough of this bombing!" and will pound the ground. This is when the second phase of battle begins. His pounds will release short, but deadly, shockwaves. If the player is hit by a shockwave, they will be paralized for about 3 seconds and will lose 1 pint of life. The player must pick up Big Bob-omb from behind (which is surprisingly very easy) and throw him. They will need to do it twice and Big Bob-omb is gone.
Whomp King (1st)
Whomp King is the boss of Whomp's Fortress. Like any old Whomp, he will try to crush you. Ground-Pound on the big X on his back to damage him. The player must then repeat this again. After they have done so, the second phase begins. Whomp King will summon two Whimps when he steps hard. Do the same thing you did in the first phase. After pounding him 2 more times, the third phase starts. His every step makes a small shockwave, and he will summon four Whimps instead of two. Pound him twice more to finish the battle.
When the Star reveals itself, the fortress rises and you must make your way up to obtain the Power Star at the top.
Captain Goombarr is completely new to Mario and is the boss of Jolly Roger Bay. Before the battle begins, he summons a robotic suit called "The Pirate's Booty". There's a problem in this battle, the Cap'n here has a sword, but you don't. Luckily, a sword is not required. What you need to do is punch and kick him. It will not do damage, but it will push him back. The battle takes place on the pirate's ship, so push him toward the edge, if successful, he catches himself and loses his sword. But then, he pulls out another. Do what you did before and drive him toward the edge of the ship. Once you do it, he catches himself again but The Pirate's Booty loses almost it's entire right arm! This is where the second phase starts. During the first phase, he held a blade-like shield thing in his left arm but never used it, now he does. He will try to "slice" you and his guard goes up. Drive him to the edge one more time and he falls off, landing in the water, cause The Pirate's Booty to malfunction and sink while Captain Goombarr drowns. The Pirate's Booty explodes, revealing the Power Star, that is now on the bow.
The second the Star lands on the bow, the back of the ship begins to sink, the player needs to quickly make it to the bow. If the player touches the water, they lose a life as if they fell into a bottomless pit. Once Mario is on the bow, the ship breaks in half and the front of the ship (the side the player is on) stays afloat while the other half sinks the the bottom of the bay.
Snowballian is the boss of Cool Cool Mountain. To defeat him, you must punch his big, red nose three times, but it's not as easy as it sounds. The giant snowball will roll around the battlefield, crushing you if it rolls over you. Swowballian is basically one the game's easiest bosses and players will not have that much of a hard time with this one. In the Master Hero version, though, this is quite hard.
King Boo is the boss of Big Boo's Haunt. This battle is just like the Super Mario 64 DS Big Boo battle, however, the mirror will show just you in the reflection instead of Luigi as in Super Mario 64 DS. But now there is a second phase, in the second phase, King Boo will teleport to a new location somewhere in the room. He will also glow blue at times and will keep charging at you really fast then goes back to normal. Do what you did in the first phase and the battle ends.
Boshi is the boss of Hazy Maze Cave. He has taken over the poor Dorrie's home and is going make him his slave. You can't let that happen! Boshi will spit blue fireballs at you and will try the swallow you. He'll also do some punches. You need to ground-pound on him three times to defeat him. After pounding him twice, he will throw spiked balls at you.
Spiny Koopa is the boss of Pipe Maze. He will go in and out of the 8 pipes on edges of the battlefield. When he completely pops out of a pipe, he begins flying in a circle, throwing balls at you. What you need to do is throw one of the ballss at him when he's flying. Repeat this 2 more times to defeat him.
Big Bully is the boss of Lethal Lava Land. This battle is like the battle againist the big Bully on the first star of Lethal Lava Land in Super Mario 64 DS. You need to drive him into the lava three times to win. After pushing him back twice, the battlefield becomes smaller.
Eyerok is the boss of Shifting Sand Land. This battle is exactly like the Super Mario 64 DS battle, however the battlefield has a new design.
The Lakitu Bros. are the boss of Skyview Falls. In the other Super Mario 64 games, the Lakitu Bros. are the camera men. In this game, they are a boss. Defeating them is sort of easy. When one swoops down, jump on their head. Once one of the bros suffers three jumps, their cloud disappears and they die. The remianing one says "HEY! No fair!" This is when the second phase begins. It's the same as the first, but the Lakitu is more fierce and swoop down more quickly. Once he is taken care of, the batle ends.
King Wiggler is the boss of Tiny-Huge Island. It's like Super Mario 64's Wiggler battle, but has a slight diference, this King Wiggler will become bigger and longer when he is furious. When defeated, instead of surrendering, he dies and leaves behind his Power Star.
Kingfin is the boss of Wet-Dry Land. This battle takes place underwater and there are plenty of air bubbles to keep you from drowning during this fight. To damage him, spin attack into him six times. After 4 hits, he summons Bone Fish.
Whomp King (2nd)
The Whomp King returns for a rematch at Tick Tock Clock. The first and second phase are just like the third phase from the previous battle. The third phase is also the same, but he will stun you if your on the ground when he pounds.
Giant Ice Piranha
Giant Ice Piranha is the boss of Snowman's Land. First, it will burrow into the ground. When this happens, Ice Piranha Plants will emerge. You need to defeat them using a Red Power Flower. Once enough plants are are defeated, they burrow into the grouind automaticly, and Giant Ice Piranha rises. Wait until it opens it's mouth, once it does, quickly shoot 5 fireballs into it's mouth, if you take too long, it will close it's mouth. Once successful or it closes it's mouth, it burrows into the ground. Repeat the attack method twice more. Once so, the second phase starts. It will stay above ground, but it attacks now. It will spit blue fireballs that will freeze you and are worth 2 pints of life if they hit you. It also opens it's mouth smaller, making it harder to shoot fireballs into it. Repeat the first phase's attack method to defeat it.
Reznors are the boss of Tall Tall Mountain. First, you must hit the large, rectangular ! Blocks each of the 3 Reznors are standing on. Hitting them will cause the Reznors to fall off, once all three are down, they will fight you. You need to ground-pound each Reznor twice to defeat it, once all three are defeated, the Star reveals itself.
Glow Boo is the boss of Flash World, you must fight him on a small battlefield the same way you defeated King Boo. Consider this as a repeat of the King Boo battle.
Lakithunder is the boss of Sky Garden. Like the Lakitu Bros. battle, you need to jump on Lakithunder's head when he swoops down. He throws down electrical Spinys, lightning spheres, and lightning bolts. Jump on his head 4 times to deeat him.
Rainbow Goomba is the boss of Rainbow Ride. You need to hit Rainbow Goomba with poison somehow. His attacks are spiting Rainbow Fireballs and Rainbow Beams and pounding on the ground. When he spits a Purple Fireball, a Purple Power Flower appears where it landed, grab it and quickly shoot Poison at Rainbow Goomba. Repeat this attack method 3 times more to win.
Bowser Jr. Bosses
This boss comes after Pipe Maze. You need to dodge his punchs and kicks. To damage him, you need to do the same, punch and kick him several times. Once you do it several times, he gets dizzy. Jump on his head. Repeat the attack method twice more to defeat him. After jumping him once, he spits fireballs and fire beams.
The boss comes after Tall Tall Mountain. This battle is a bit different than your previous encounter with him. He now wields a powerful brush that he calls the "Power Paintbrush". Now he shoots poisonious graffiti from the brush and it's a lot harder to damage him. Otherwise it's the same as last time.
This boss comes after Jolly Roger Bay and takes place in Bowser in the Dark World. Bowser Battles are similar to battles in Super Mario 64. So the game plan is to get behind him, grab his tail and swing him into one of the spiked mimes. But in Super Mario 99, you need to swing him into two to defeat him.
This boss comes after Shifting Sand Land and takes place in Bowser in the Fire Sea. The battle here is the same as the Bowser in the Fire Sea one from Super Mario 64 DS. The battlefield tilts everytime Bowser pounds the ground. He also teleports and charges at you. Otherwise this battle is the same as last time.
This boss comes after Tick Tock Clock and takes place in Bowser in the Sky. Instead of what it was in Super Mario 64, it's like your battle from last time at the Fire Sea. What changes is that the battlefield is on poison water instead of lava and kills you with a single touch. Also, you now need to swing him into three mines instead of two. Otherwise it's the same the previous two encounters.
Battle 4 (Final Boss)
This boss is after the final course and takes place in Bowser's Last Stand. The battle is the same as your previous battle with him. The battlefield no longer tilts and Bowser pounds cause huge shockwaves. Once he's hit by three mines, a cutscene kicks in where Bowser falls off the battlefield. Then, all of a sudden...
...Bowser rises at a superior size! He will pound the battlefield with his fists and make shockwaves doing so. He also throws spiked balls, when a green one hits the ground, it reveals a Green Power Flower, get it and throw a spiked ball at Bowser. You need to do this 9 times to defeat Bowser once and for all.