In Bowser's Castle, the Bowser Jrs. wonder what to do with the book. Bowser Jr. wants to throw it away. Paper Bowser Jr. agrees. Bowser Jr. has second thoughts after a while. He thinks it may come in handy. Perhaps they will terrorize the paper world. He wants to show it to Bowser. The Bowsers are pleased with Mario's destruction and Kamek says the plan involving the Toads working underground is proceeding nicely. Bowser Jr. tries to talk to Bowser, but Bowser talks to Paper Bowser Jr., thinking he's his son. The Bowsers are too busy to deal with their sons and tell them to stay on guard duty. They throw temper tantrums. Kamek suggests sending them to the villa. Paper Kamek says the papercraft should provide a diversion. Paper Bowser makes it sound like a surprise, so their sons agree to go to the villa.
Elsewhere, the princesses are plotting their escape. Paper Peach has a spare cardboard cutout of herself. She thinks Bowsers' sons won't notice. Peach is tired of getting kidnapped (and everyone else is tired of her getting kidnapped). Flying in the clown car isn't so bad, but can't stand saying "Save me, Mario" another time. Peach asks Paper Peach if she feels the same. The Bowser Jrs. say they're leaving for the villa and the princesses are coming with them.
The bros leave through the gate in Twinsy Tropics Dungeon. They're still in the dungeon, however. There are Paper Scaredy Rats here. There's some of that mysterious ore that the Toads keep mentioning. Use the Trio Hammer to break them. They may give you coins. Nearby, use the Trio Grab to grab the yellow platforms on the other side of the water to form a bridge. Go north and you'll find Bowser's emblem. Luigi finds it suspicious. He suggests they should remember this exact spot because this type of adventure has some sort of foreshadowing device. He's also worried about the abducted Toads. Mario thinks the wall is connected to Bowser's Castle, but Starlow's not sure how.
After the fourth wall is broken, walk to the left to find a couple of Toads carrying the ore near a conveyor belt. They toss it onto the conveyor belt and collapse. They say it's hard work and the ore is shipped directly to Bowser's Castle. They inform the bros there's a pipe past here, but it's guarded. Roy appears and tells the Toads to stop slacking off. He thinks the area's given up all its ore. He tells them they're not paying the Toads to chat, or at all for that matter. He leaves and the Toads say they're cheering for the bros. Go south. Use the Trio Grab to form more bridges near the circles in the ground.
Go west to find more prison cells. Behind the wall is a block. There's a Paper Goomba in a cell. It's the Paper Goomba the bros crumpled a couple of times earlier. After his defeat, he was deemed unfit as a minion according to management. He got demoted to janitor and is cleaning cells. It's all the bros' fault. He also accidently locked himself in the cell. The bros try to walk away, but ihe wants to escape and not work for Bowser anymore. He promises a reward and to forget what the bros did to him. He slides them a battle card set. In return, Paper Mario shows him how to flip sideways. Two Hammer Bros appear. The Paper Goomba runs off as the battle starts, but reappears to teach about battle cards. A new card will be dealt from your set each turn. Star Points are required to used the cards as indicated on each card. Battle to get more Star Points by filling the meter. Only 3 cards can be out at once. You can flip cards over if you don't want them to free up a slot. After the battle, the Paper Goomba will show you the battle card menu. To use a card, it must be registered to a set, which can have only 10 cards. Registered cards have a check mark on them. After the tutorial, the Paper Goomba leaves, saying perhaps they will meet again. In the left cell, there's a crack in the wall, but the Toad won't move, saying it's his ticket to freedom. Go south to form a bridge, return and go west.
There are more enemies and ore here. Form the bridge and go west. Starlow spies a pipe ahead. Walk to the south to form more bridges. One requires going under a stone bridge to reach it. Walk up to the pipe and Roy and Wendy drop in. She says they could've stayed in their cell, but were inconsiderate for making them chase them. Roy calls for Larry, but he doesn't appear. Roy thinks he may be playing videogames. Wendy will toss rings for the bros to dodge. Roy tosses rocks. Successfully counter and the rock will hit Wendy. She will then attack Roy. They can also team up to launch their shells. Counter with the hammer. After a while, the two will get angry and chase the bros. Wendy will breathe fire to take out Paper Mario, so be sure to dodge. Use the Airplane Dodge to dodge the giant ball Roy throws. If Roy holds a rock over his head without attacking, attack to make him drop it. Keep yourself healed. If you defeat Wendy first, Roy will attack with magic. A giant ball of magic will fall on a bro. Counter with the hammer.
Wendy blames their defeat on Larry's absence. The two leave, and before the bros can make their escape, the Toads stampede to freedom. Before the bros do the same, we backtrack to the cell with the crack. Send Paper Mario to the block behind the wall for some 1-up Mushrooms. Take the pipe out of this depressing place.