- The opening — Toadstool is kidnapped, so Mario Storms The Castle and fights his way to Bowser in under five minutes. For that matter, the duel with Bowser is great in spite of its ease, Mario and Bowser battling atop chandeliers in Bowser's throne room, Toadstool strung up between them. And Mario wins by knocking out the Chain Chomp holding up Bowser's chandelier, sending him to a Disney Villain Death. The entire set piece genuinely feels like a final boss in any other Mario game.
- On top of that, just to show this isn't like any other Mario game before, as soon as Bowser is defeated, a giant sword with eyes suddenly descends from the heavens and stabs into Bowser's Castle, sending Mario, Toadstool and Bowser across the kingdom. To reiterate: the game starts with the usual Mario vs. Bowser skirmish, and then introduces its main villains after Mario has seemingly won.
- Most of the boss fights with the members of Smithy's gang, due to their challenge level, awesome designs, and the fantastic boss music.
- Mack the Knife, a Wake-Up Call Boss for the rest of the game after the Hammer Brothers and Croco. He attacks with four of his Shysters, can use the group-hitting Flame Wall, and jump and stab you for one of his other attacks.
- Bowyer is one of the few Puzzle Bosses in the game, as he will lock your A, X, or Y commands, preventing usage of attacks, items, or special attacks. Beating him requires you to not only be strong, but smart.
- Yaridovich may be That One Boss, but damn if he doesn't work as a climactic end to the quest for the fifth Star Piece and make you fight like hell to get it back from him.
- The Axem Rangers, a parody of Power Rangers / Super Sentai that you fight three-on-five atop their airship, the Blade. And then when you beat them, they activate the airship's primary weapon, the Breaker Beam. It is not unexpected to see a party member drop to the ground after it hits.
- The battle with Exor atop Bowser's Keep, Mario and his allies leaping into the fray atop a turret to face the giant sword face-to-face. The entire game has been building to this fight, and it's another Puzzle Boss with you having to incapacitate the eyes on the crossguard to damage the real target, the face on the pommel. Which happens to be the only boss in the game vulnerable to a timed hit from Geno Whirl, allowing you to deal it a One-Hit KO.
- The final battle with Smithy himself. He's a shapeshifter who will rotate his head through various attack forms to debuff you, use One-Hit KO attacks, heal himself, deal devestating group attacks, and inflict status ailments on you. At 8,000 HP he has double the health of any other boss in the game, so prepare for a long, epic brawl.
- For the first time in Mario history (unless you count Super Mario Kart), Bowser is playable. For that matter, Toadstool is playable too. Players can make the iconic trio a party and bring the pain on Smithy and his forces.
- Bowser joins the party when he sees Mario stopped cold by a locked door. Bowser's response is to snap his fingers and slam his shell into it to smash it down.
- As much as he's an Ineffectual Sympathetic Villain in this game, Bowser still terrifies the civilians of the Mushroom Kingdom. They panic at just the sight of him, and a growl sends them fleeing to hide shaking in the corners of the room.
- When Mario gets to Bowser's Keep the second time, if Bowser is included in the battle, certain enemies will flee at the sight of him.
- Toadstool refuses to sit on her keister letting Mario save the world this time, so she has her grandmother disguise herself as her so she can sneak out of the castle and join Mario's adventure.
- The boss battle with Johnny Jones. At first he's nothing special, just another boss with a force of flunkies backing him up. Then after he Turns Red and you dispatch his flunkies, he's impressed with Mario's skill and challenges him to a Duel Boss battle. It's the first time since the Hammer Brothers fight at the start of the game that Mario has fought solo, and he single-handedly beats Johnny and wins the Star Piece.
- There's a tiny one which doubles as a subtle Heartwarming Moment. When you first meet Mallow, his adoptive grandfather's coin's just been stolen, and, though he has been raised as a frog, he cannot jump. 6 stars' (and one recovered coin) worth of adventure later, Mallow's discovered that he's a prince, has found his true mother and father, and when he needs to jump onto the skybus taking the party to Bowser's Keep.... he does so. With aplomb.
- Culex, a boss ripped straight from Final Fantasy that would invade Mario's world if he had the capabilities. Mario and his allies defeat him and prove themselves just as badass and powerful as any Final Fantasy hero, and are rewarded with the Final Fantasy IV Victory Fanfare and the series' iconic Prelude theme in the scene afterward.
- Midas River 100 coin run.
- Being hit by one of Bowyer's arrows and turned into a scarecrow prevents physical attacks, but not special ones. So your team of scarecrows can still cast lightning and shoot laser beams.
Awesome / Super Mario RPG