Babbo is cracking and needs to be taken to Caldia to get repaired. Belle, Alviss, Dorothy, and Ginta decide to take Andarta to get there. Pinocchion shows up and attacks Dorothy, destroying her Andarta. Kouga shows up to fight Alviss, and Giromu attacks Ginta, almost killing him. Team MÄR defeats their enemy and continue on their way to Caldia on Ed's Magic Carpet.

Girom, Kouga, and Pinnochion attack Caldia in plans to capture the Caldia Grand Elder. Dorothy and Ginta, however, show up and defeat the three.

Ian pursues Chimera in hopes to defeat her and reverse Gido's transformation. Chimera is more than a match for Ian at first, though Ian gains the upper hand by cleverly using his Moon Fall. Finally showing humanity, Chimera, before dying, breaks the curse on Gido, and wishes for the two to have a happy life together. Chimera is last seen with her eyes back to her own normal, compassionate eyes.

With the help of Pozun's Andarta, Ginta and the rest of Team MÄR storm Lestava castle to rescue Snow. To get to Snow, they must first have to go through a barrier of Chess Pieces and among them, the one responsible for Snow's kidnapping, the Knight Magical Roe. Magical Roe, once defeated by Ginta and Alan, realizes his wrongdoings and chooses to die to save the princess, much to the two's shock.

On their way to banish Phantom from existence once and for all, Dorothy and Alviss are waylaid by their target's remaining most devoted minions, Candice and Rolan.

Phantom reveals his final efforts to defeat Team MÄR, the Ghost Chess, a powerful group of Ghost ÄRM users most loyal to Phantom. Their leader, Kapel Meister uses a Ghost ÄRM to speed up the process of Alviss' Zombie Tattoo.

MÄR manage to meet up with each other, and Nanashi finds a map. On the map is the island of Pultgayin. The party deduces that this is the lair of the Ghost Chess. Nanashi uses some strange thief skills to get the team onto the island, but his raft is destroyed on the way there, and Allan has to throw the team using his guardian. Meanwhile Kapellmeister steals Alviss away from Belle and Snow. With that success, the Ghost Chess are called to retreat, but before they leave, the Flat Sisters merge with a Ghost Guardian and attack the team.

MÄR learns that Poko has found an underground entrance to the island, and they take his whale to enter undetected. Meanwhile Alviss is on his way to see Phantom. Rolan doesn't trust Alviss' change in heart and tried to prevent him from meeting Phantom. Once Alviss meets Phantom, Alviss begins to feel drawn towards the dark side. He quickly attacks Phantom and tries to insert the key into Phantom's chest, but Phantom is too powerful and easily stops him. The episode ends with Alviss on a chain leash that Phantom is holding.

With Alviss's Zombie Tattoo causing him to fall under Phantom's control, the others end up fighting Alviss.

Ginta, Dorothy and Belle approach the coliseum. They are met inside by the Misty Knights and Misty Hadju. When they refuse to leave, the Misty Knights vow to kill them. Meanwhile Loco swaps bodies with General so Chaton can be dragged into the prison to be with Alan. Alan and Nanashi have become test rats for a Ghost ÄRM experiment meant to remove the need for human emotions from Phantom. Just before the Misty Knights attack Ginta and Dorothy again, the ghost ship from Vestry arrives and advises the Knights that they have been fooled by the Ghost Chess. Ginta and Dorothy learn that Alviss himself will have to arrive before the path to Clavier will open.

Team MÄR ends up captured by the Ghost Chess alongside Loco and Chaton.

Team MÄR head to the coliseum with Alviss. They are met there by the Ghost Chess, they fight to let Alviss through to the Clavier. Loco sacrifices the last of her magical power to save Chaton, and ends up as a baby. Alviss makes it to Clavier, where he meets up with a small boy, wanting to save MÄR Heaven. Alviss lets the boy take the ÄRM. (We get hints that the boy is actually a younger Alviss.)

Team MÄR hold back Kapellmeister and the Ghost Chess from following Alviss into Clavier. During the battle, Sara's use of her Ghost ÄRM ends up destroying her. Seeing that his Ghost Chess members cannot defeat MÄR, Kapell absorbs them into his body in order to activate his ultimate Ghost ÄRM. MÄR quickly defeats him.

Alviss, Ginta and Dorothy head back to the castle to kill Phantom. They were stopped by Rolan, who said only Alviss could go forward with him. When both of them reached the throne room, Phantom, along with Candice, had disappeared. Enraged, Rolan tried to kill Alviss, but stopped when he heard the teen cry out in pain. Using a sharpened vine, Rolan stabbed himself to death, wishing that he and Phantom could meet again in a more peaceful reborn life. Alviss, Ginta and Dorothy heads off after Phantom. Candice tried to stop them from killing Phantom, but failed. When Alviss was about to kill Phantom, he hesitated, and Phantom plunged the Prifickave into his own body, thus ending his own immortal life, much to Alviss's shock. Alviss is freed from the Zombie Tattoo.

The truth of Snow is finally revealed, that she is connected to Koyuki of Earth through the evilness of Diana, who planted a Magical Stone in Snow's mother to make it all happen. Using their connection, Diana plans to open a portal between both worlds.

The Chess Pieces' King finally reveals himself in a final attempt to bring the world under his control. To begin his plot, King kills Alan with ease. Before dying, Alan gives his final words to Team MÄR and gives Chaton his earring.

Ginta and Dorothy head to Caldia and end up freeing Caldia's Grand Elder after Diana's attack. Meanwhile, Alviss, Jack, Snow, and Nanashi re-encounter Pano who was stealing food. When Garon and Leno end up with the same fate as Alan, they are attacked by King. Nanashi and Snow end up becoming his next victims.

After Nanashi and Snow's death, Ginta, Alviss, Dorothy, Ian, and Ash discover King's plan to take over Earth. When King attacks, Ash becomes his next victim. He leaves behind a mysterious ÄRM.

Alviss faces off against King and discovers that his identity is Danna Toramizu, Ginta's father and the one who helped save MÄR-Heaven six years ago. When Alviss was about to die in King's hands, he saw Rolan and Phantom, who encouraged him to stand up and fight, and so did Bell (although she did not know they were there). Alviss sacrificed himself by holding King down so that his ÄRM a Baoa Qu could activate and blow King (along with him) up. King escapes, but Alviss is severely wounded. Before dying, Alviss uses the last of his magical power to activate the ÄRM that Ash left behind. When Dorothy, Ginta, and Babbo leave to go to the stolen Caldian castle, Alviss thanks Bell and dies.

After Alviss' death, Ginta, Babbo, and Dorothy head toward the stolen Caldian Floating Castle where King is hiding. Once there, Dorothy faces off against Diana. Once Diana is defeated and killed, King Danna-Orb arrives and kills her.

After Dorothy's death after the death of Diana, Ginta faces off against the Chess Piece King Danna-Orb. During battle, Ginta discovers that his father's soul was within Babbo all along while Caldia's Orb was in Danna's body. After Caldia's Orb is removed from Danna, Caldia's Orb takes on its true form and invades Earth.

With Caldia's Orb on Earth, Ginta takes Babbo's Gargoyle to Earth for the final battle. The two end up in Tokyo, where their battle eradicates the city and destroys a large part of the population. Snow's spirit, however, combines with Koyuki's to form one being, and by doing so removing the magical stone from Snow. Ginta uses the stone to create a more powerful Gargoyle that uses the hopes of MÄR-Heaven to defeat the Orb once and for all. With the Orb destroyed, peace brought to MÄR-Heaven, everyone who was killed by King revived, and Danna restored, Ginta returns to his own world with his father. At the very end, Ginta and Koyuki, who has fused into one being with Snow, walk home together at sunset. She clings to his arm and they both blush.