They come back out just in time - Phantom wants to begin the final battle on the next day.

Jack fights first against Weasel, the man who killed his father in the first War Games, and he wins. Alviss is next, and he goes up against Rolan for a rematch. This time, the fight is more intense; they both feel that they are fighting for the sake of their ideals; Alviss treasuring his mortality, and Rolan idolising eternity. Alviss spends the beginning of the match refusing to fight, hoping that Rolan will be convinced to see the reality behind Phantom's "eternity", but the battle finally turns serious, and they put all of their efforts into winning. Although Alviss tries again to lure Rolan to his side, and he comes very close to succeeding, in the end they're unable to reconcile, and they each use their Guardian ÄRM in a final attack - and Alviss emerges the victor, without killing Rolan.

The battles continue, each taking place on a separate day. Dorothy defeats Chimera, Alan wins against Halloween after drawing with him six years ago, and Nanashi gets his revenge on Peta for killing the thieves of Luberia. Finally, the last match comes - Phantom vs Ginta. Even though the score is 5-0, this is the only battle that actually matters, because they are both captains. The fight is long, intense, and close on both sides, but in the end, Ginta wins, and the Chess Pieces lose the War Games for good. They reluctantly retreat, and Team MÄR's next target is Lestava Castle, where Snow is being held captive by the Queen. However, before that, Alviss, Ginta and Dorothy have to go to Caldea to repair a crack that Phantom made in Babbo. While they're there, Ginta asks the Caldean Elder about a key-shaped ÄRM he got from a ghost at the start of his journey; the Elder explains that it's Purific Ave, and it is the only thing capable of killing Phantom for good. Alviss asks to keep the Ave, wanting to kill Phantom himself.

Finally, Team MÄR makes it to Lestava Castle to save Snow and kill the Queen. They split up when they make it inside; Alviss and Dorothy deal with the guards so that they can beat Phantom and Queen Diana separately, but they're attacked by Rolan and Candice before they can reach Phantom. When they finally win after a long struggle, a new opponent shows up, and he hits Alviss with a Ghost ÄRM called the Rondo of Time, which speeds up the progress of Alviss' Zombie Tattoo significantly. The newcomer uses a Dimensional ÄRM to transport them all to a desert - where they all have to fight to restrain Alviss, who is being driven mad by the pain from his now near-complete Tattoo. Snow and Ginta use their Sacred ÄRM to suppress the pain, but the Rondo of Time cannot be stopped, and as another side-effect of the Tattoo's progress, Alviss experiences a connection with Phantom, who commands him to come to his side, although for the moment, Alviss resists.

Team MÄR soon learns that the man who used the Rondo of Time is one of the Ghost Chess, a group that exists only to please Phantom, and it just so happens that what will please Phantom most is to have Alviss, so they move out to capture him. Unfortunately, the others have to fight back on their own, because Alviss is incapacitated by the effects of the Zombie Tattoo. When the head of the Ghost Chess comes to retrieve Alviss, he appears to have been completely taken over by Phantom's influence, and he submits to the summons. However, once inside the castle, Alviss manages to overcome the possession, and he attempts to stab Phantom with the Purific Ave - unsuccessfully. Phantom deflects him, and he uses the bond he has with Alviss to put him under a sort of mind control. He collars Alviss and chains him to his side.

Alviss is self-aware for half of his time in captivity, but for the rest, he is completely under the control of the Zombie Tattoo and Phantom. The influence is so strong that he attempts to kill Team MÄR when they come to retrieve him, and barely manages to control himself for long enough to let them escape. As he is left in isolation, though, his determination allows him to direct his violent urges elsewhere - he breaks out of Phantom's tower and attacks the Ghost Chess who were attacking Ginta and Dorothy before turning on his friends, hoping that they will kill him. Thankfully, Snow hits the Rondo of Time with ice, freezing it and allowing Alviss to recover his sanity and control.

However, the Tattoo is extremely close to completion, and he still suffers bouts of madness, but Team MÄR refuses to let him give in, and they take him to the Misty Castle, Clavier, in order for him to acquire the Almetici ÄRM that is capable of granting any wish. When he reaches it, he encounters a younger version of himself, who says that he needs the ÄRM to save all of MÄR Heaven. Alviss feels that this is more noble than his current wish, and he gives up the ÄRM, but when the child receives the ÄRM, he finds that it is only a dagger - the same dagger that Alviss used to break open the gates of MÄR Heaven when he summoned Ginta. He hands the dagger to the child and tells him to hang onto it before he goes back down to the others, the Rondo of Time beginning to tick again.

Alviss returns from Clavier just in time to help everyone after the defeat of the last member of the Ghost Chess, but he is in a critical state due to the Zombie Tattoo, and Ginta carries him to Phantom's castle, where they find Rolan. Alviss allows Rolan to take him to the throne room, and when they see that Phantom is missing, Rolan assumes that he died in Alviss' absence; he promptly commits suicide in front of Alviss, who takes a moment to mourn him before they go on to find Phantom. (It's revealed in the ending of the series that Rolan survived, but Alviss remains unaware of this.) When they reach him, he has changed - he appears to be terribly ill, barely capable of movement, and he has lost his love for immortality, regretting the things he has done in his life. Phantom welcomes his own death, going so far as to help with the killing strike when his sudden kindness causes Alviss to hesitate. Alviss lays Phantom's body to rest and asks Jack to grow a field of flowers around it, so that Phantom might rest in peace.

Finally, they make their way to Lestava Castle to kill the Queen and King at last, but both have already moved on, and instead, they meet Snow's father, the King of Lestava, and have a party to celebrate the defeat of the Chess Pieces. In the middle of their celebrations, there are suddenly reports of catastrophes in surrounding towns, and when they go to investigate, they find that famous Earth landmarks such as the Eiffel Tower are being dropped from the sky. When they return, they learn that the King attacked Lestava while they were gone, and Alan was killed in the ensuing fight.

Ginta and Dorothy go to Caldea to ask the Elder about what is happening to MÄR Heaven, while Alviss and the others go to look for information in town. They encounter the King there; Nanashi is killed trying to protect his friends, and when Alviss tries to escape with Snow, she is also mortally wounded. However, the King leaves Alviss alive, so he immediately escapes to Caldea with Snow, Jack and Jack's girlfriend Pano, and Snow dies in Ginta's arms when they arrive.

Abnormalities continue to happen all over MÄR Heaven, and the remaining members of Team MÄR do what they can to help villages and citizens, but they continue to lose friends to the King. Alviss, Dorothy and Ginta go to an island in order to activate an ÄRM that will take them to where the Queen and King are, and while they're there, Alviss runs into the King, and he fights him. While the King initially appears to be Boss, Alviss comes to the conclusion that it is only a resemblance, and fights with all of his strength; he does a lot of damage to the King, but is badly wounded, and he sacrifices the last of his life to complete the activation of the ÄRM that Dorothy and Ginta had worked on. He sees the two of them off, and dies once they have gone.

Dorothy kills Queen Diana before getting killed herself by the King, and Ginta takes a last stand against the King. In the process, he finds out that while the Orb of Caldea - the sentient concentrated evil of everyone in MÄR Heaven - took his father, Boss', body, Boss' soul was transferred into Babbo at the same time. Ginta defeats the King, which ejects the Orb from Boss' body, and he puts Boss' soul back into it before he heads off to destroy the Orb. The bonds with all of the people he has met in MÄR Heaven give him the strength to win, and he creates a new power for Babbo that revives all of his dead team-mates. With the Orb gone, MÄR Heaven is finally at peace, and Ginta spends some time helping to rebuild the world with the rest of Team MÄR.

Even though everyone wants Ginta to stay with them in MÄR Heaven, he and Boss have to return to Earth, where their old lives are waiting for them. Dorothy finds another Gate Keeper Clown to take them back, and after exchanging farewells with everyone, they head home. The series' ending montage implies that Alviss goes on to live with Bell, keeping contact with the friends he has made during the War Games and training in case the peace of MÄR Heaven is ever threatened again.