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Mario and Pyrouge return to town and find a Toad with an odd blue flame around him. The Toad then says "All creatures will suffer the wrath of the Embers!" and attacks the 2. They easily defeat the Toad and an Ember pops out of him. Pyrouge is about to obliterate the Ember, but he stops as the Ember tells him that he was actually just looking for someone to take him to his home at Keel Jungle. Pyrouge is reluctant to help, but Mario gets a text that says the next meddalion is at a jungle, so he offers a hand. Mario and Pyrouge visit the castle and use their newly created Medallion to weaken the forcefield. They do so, but realize that they need 6 more to break the seal.They visit Merlon and he tells them that to get to the Jungle, they will need help from Salty Spiny, who can build them a ship. They visit him near the bay. Salty dosen't want to help them, but is harrased by Pyrouge and Ember until he does. He readies his tools, but finds out that he is out of supplies. He needs 20 pieces of wood, 10 nails, and a cool symbol for the ship. Mario and Pyrouge search for the wood near the bay and find 10 pieces of driftwood. They then stop by the shop and purchase 2 2x4's to use. While looking for more wood, they meet a lumberjack who would work for a nice meal. Mario gives him some of their rations and he cuts down 8 trees that were blocking a pathway. They hand the wood over to Salty and he demands nails, which Pyrouge will only get if he says "Please". He dosen't, but Pyrouge decides to help anyways. They visit the Pawn Shop, but don't see any nails for sale. Pyrouge does see a hammer upgrade for Mario, so they trade for that instead. The hammer can break down Stone blocks and take out nails. Mario uses this to take nails out of various locations around Toad Town. They hand the nails to Salty, but he still needs a cool design. Mario & Pyrouge don't know how to make a cool design, as only an artist or computer nerd could make a design that Salty Spiny wouldn't spit at. They return to the pathway that the lumberjack cut down, and find a dusty old house with a Toad Nerd in it. He thanks the two for cutting down those fast growing trees, and gratefully lets them use his computer to make a design (here the player can make their own design a l'a Animal Crossing). They hand the design over to Salty (who questions their artistic skills) and put it on the sail. Salty is now finished with the ship (although it's really just a poorly designed raft) and allows the heroes to use it whenever they please. They use it, get shipwrecked in a storm, and get marooned on Keel Island.
Pyrouge and Mario try to collect themselves as Ember looks for his friends. Mario decides that they'll find the medallion pieces faster if they split up. Mario heads north and finds an ancient Mayo Temple which can be opened with a switch at the top. His partner says that they need someone who can go high enough to hit the switch. They continue on and end up in the Infinite Maze. The maze has a barrier around it that prevents anyone from cheating. In the maze they meet a Torpedo Ted named Terpedro. He got stuck in the maze when he left the Torpedo Base in search of a Wi-fi hotspot to play Mario Kart DS online. He agrees to help Mario if he gives him his friend code. He does so and uses Terpedro's projectile abilities to escape the maze. They reach the sunken Torpedo Base where all other reformed Torpedo Ted's hangout. Mario stocks up and returns to the temple, which he can now open.
In the temple, Mario uses his new hammer and Torpedo friend to make it through many traps. They eventually meet a severly hurt Goomba that tells of a great evil which stole his life force. They here rumbling and flee as a Mega Fuzzy approaches the Goomba and steals his remaining life force and grows larger in size. They continue on through the temple until they find the throne room, where they meet the ghost of King Mayonaisen. He says that he found an odd green shard that he found in his tomb. The shard has been keeping him from his eternal slumber so he decides to give it to Mario. He is about to give it to Mario as the Mega Fuzzy steals his power (he's dead so he has no life force)and then fights Mario for the Medallion Shard. The Fuzzy fights by stealing energy and running over Mario and co., but is eventually defeated and life is returned to the weak. The King gives Mario his Medallion and the story cuts to Pyrouge.
Pyrouge is relaxing at the shore, glad to finally get a break, when he suddendly hears Ember scream. He follows the East Path and sees 2 Piranha Plants harrasing Ember. Pyrouge steps in and fights the plants when he is stopped by a Piranha Plant with a bandana and sunglasses called Pirappa who breaks up the fight. Ember goes off to find his friends again as Pyrouge tries to find the next Meddalion shard until 2 green Piranha Plant Guardians that hinder his progress. He asks how he will be able to pass and they say that Pyrouge needs to get permission from their leader, Pirappa. Pyrouge finds an underground chasm and eventually finds Pirappa's hidout. Pyrouge asks him to join them on their quest, but he explains that he is pacifist and refuses to fight. Just then 2 Lava Bubbles appear, exclaiming that they have finally hunted Pirappa down. Pyrouge defeats the Bubbles and Pirappa realizes that he is not causing peace by not doing anything and joins Pyrouges team. Pirappa can plant his routes in fertile soil to remove live vines from his path. Pyrouge later travels farther till they see a rock wall and have to turn back. Just then, a trap is initiated and they end up in the lair of Mowzer, expert bomb fighter. He agrees to help if they can solve his 3 puzzle. After some frustrating challenges, they earn the kinship of the young Squeak. Mowzer attacks by slapping and can place bombs outside of battle. They exit his lair and bomb the wall revealing a giant Refelsa Plant, an extinct ancestor of Piranha Plants. The Refelsa Plant swallows the heated hero and he ends up in its body.
Pyrouge wakes up in Stomach Acids and narrowly escapes getting digested. He travels through the body using the abilities of his newly aquired friends and eventually makes it to the Brain. The Brain explains that the Medallion Piece is in the heart and is the reason the plant hasn't died. The piece has also made the plant evil and the Brain urges Pyrouge to remove it, even if it means death. Pyrouge explores the plants body and finds that the medallion has been creating shadowy stomach bugs that have been causing the Refelsa Plant to become evil. Pyrouge defeats most of the bugs and makes it to the heart cavern. Here they see numerous bugs forming to make one Demon Bug. The Demon Bug swallows the medallion piece and is able to create moe Shadow Bugs. Pyrouge puts up a long and painful battle with the Demon Bug and eventually seems to defeat it, but because it swallowed the green meddalion piece, it will continue to reform and cannot be defeated. Just as all hope is lost, Ember bursts through the Refelsa Plant's heart and takes the meddalion shard and gives it to Pyrouge. Pyrouge then deals the final blow and the Refelsa Plant dies and is spat out to where Mario is. They reunite their pieces and the chapter ends.
Peach is then shown to be spying on Bowser and Darkly again as they are playing Super Smash Bros. Brawl to ease their stress. They are playing as themselves against Mario and Pyrouge, but lose. Darkly asks where the bronze meddalion shards are and Bowser says they are high in the sky, far away from Mario's reach. Darkly then asks if he thinks it will be safe there as the last place was still found by Mario and Pyrouge and that if they find a Star Medallion again, he will take matters into his own hands. Peach flees to her room and contacts Mario about this.