Fighting off the gigantic enemy papercrafts by using a different papercraft each time. One of them is actually Papercraft Peach.
The Peaches aren't idle throughout the game and attempt to escape the Bowsers on their own. They almost do so while guarded by the Bowser Juniors.
The Goomba bully, after being betrayed by his own allies, teaches the Bros how to use Battle Cards while temporarily on their side.
Ludwig and Larry decide to use Battle Cards against Mario and Luigi just like they have been using in the past.
This is a villainous example: late in the game, both Bowsers get a particular moment. After lifting their castle from the ground and calling it Neo Bowser Castle, they fire cannonballs at Peach's castle, completely obliterating it. And what Bowser says beforehand is also awesome and yet adorable at the same time:
Later turned into a CMOA for Team Mario! The Koopalings later take aim at Peach's Castle one more time with the gigantic main cannon of Neo Bowser Castle, aiming to snuff her out and wipe it off the map. What are our heroes to do? Nuttin' but whip out their hammers and cave in that sucker's barrel!
Luigi saves his brother from Boos in spite of his fear. Then both of them save Paper Mario by fighting King Boo together.
Right before the Neo-Bowser's Castle, King Bob-Omb faces the Bros alone, attempting to blow himself and the intruders up. They manage to defeat him in time regardless.
The final Nabbit chase is full of this:
Whenever you catch him, he actually fights back. He attacks the Bros. by chucking out a bunch of objects stored in his Bag of Holding, including spiked balls and paper enemies. He even weaponizes the bag itself with a hammer throw.
Should Nabbit run into an enemy, the Marios are forced to do battle with it as normal. Here's the kicker: Rather than immediately fleeing and saving his own skin, he instead joins the Mario Bros. in battle to take down the enemy. Nabbit acts as a computer-controlled "fourth" party member in these fights; he attacks with a stomp move similar to that of Mario and Luigi, heals all three of the Bros. with mushrooms if necessary, and even has his own Bros. Attack with them!
Luigi's final Bros Attack, which you unlock from the above: Mega Thwonk. Luigi eats a Mega Mushroom and turns into Giant Luigi from Dream Team, runs up to the enemies in a Rhythm Game, smashes them out of the park with his hammer, then Mario jumps on them repeatedly, and if done perfectly drives them into the ground on the last stomp, causing them to skid across the ground for a ton of 1 damage hits, followed by Giant Luigi giving a thumbs up. For bonus points, this is one of the few Bros Attacks where Luigi isn't the Butt-Monkey, and it's easily one of the most damaging attacks in the game. It also works on the Final Boss!
In the final stretch, the Bowsers decide to nip your antics in the bud, revealing they've taken all your Papercrafts. Unleashing their secret weapon, the gigantic Papercraft Bowser, they then burn all your precious Papercrafts to cinders — right before poor Toadette's eyes, who's brought to tears. However, she's soon struck with inspiration, requesting the Marios and Luigi go fetch the Fire Ore around Neo Bowser Castle. Upon delivering it, Toadette sets off to work. However, the Bowsers have not been idle, and prepare to finish off their adversaries with a Papercraft Banzai Bill cannon. However, suddenly, a bouncing fireball! And a second one, destroying the cannon! Behold, Toadette's masterpiece and the colossus to trump the fire-spewing titan at the Bowsers' disposal: Papercraft Fire Mario!
But speaking of Bowser nipping you in the bud, props to him for being much more proactive about you invading his castle than he was in other games, let alone earlier in the game. The final gauntlet of enemy waves and the Koopalings also serves as a moment for his minions, they're really putting everything in stopping you.
Morton takes precautions during his boss fight with him as well as Iggy and Lemmy and uses his magic to disable your Battle Cards. Even your amiibo ones if you're using them too.
The dialogue leading up to the first phase of the final battle is pretty epic in and of itself, setting up for a climactic no-holds barred slugfest between the parallel Marios and Bowsers! And a green gu-- I mean, Luigi.
Paper Bowser: So, Mario... Paper Mario: *Gameface on!* Bowser: And...other Mario! And Luigi... Mario & Luigi: *Battle stance!* Bowsers: *Charging forward!* LET'S DO THIS!
The Final Boss, as both series are oft to be good about. Okay, so everyone and their grandmother saw a Bowser Fusion coming a mile away... But nobody saw this coming. Giant Bowser of the real world, wearing the giant cardboard Bowser from the end of Sticker Star as a set of mechanized armor, Shiny Robo-Bowser! The real clincher is that Paper Bowser in this state can shapeshift like Paper Mario, unleashing similarly devastating techniques. Not only that, they have a version of your Trio Attacks! In fact, if you try to use them while the head is still active, they'll unleash theirs and break yours!
Special mention goes to one of the counter attack sequences once Bowser's health is low. Bowser attacks with a modified version of his stomp attack, and after the Bros manage to counter each of his stomps, he quickly follows up with a full-power spinning dropkick... And the Bro that counters it manages to hold him off COMPLETELY as they're skidding back across the battlefield, and potentially able to completely counter the dropkick if the player is able to Button Mash fast enough successfully.
Bowser (or rather, both of him) actually manages to be an incredibly chilling villain in spite of his comedic moments, finally fully developing from the buffoon he was back in Superstar Saga. Judging by some of his dialogue and his wordings, he is now running on oft Tranquil Fury which is genuinely far scarier than his Large Ham tendencies. He also manages to pull off several malicious deeds, such as having Toads work as slave miners, carpet bomb Peach's castle, destroy all the Papercrafts, and even plan to ensure a Deader than Dead fate for the heroic trio via trapping them in the now empty Paper Mario world, and destroy it right then and there. Since his awesome heroic outing in Bowser's Inside Story and his magnificent showing in Dream Team, Bowser just got better and better at his A-game.
