Ginta Toramizu, an otaku-ish high school student, has had his 102nd dream of a fantasy world that goes by the name of MÄR-Heaven, and is subsequently subjected to many jeers from his classmates because of that, save for his childhood friend Koyuki. One day when he is briefing her on his newest dream, a phantom clown appears and claims him as the chosen Earth dweller to be permitted entrance into that very same wonderland. His embarkment into MÄR-Heaven is greeted by the meeting with a mysterious, beautiful witch named Dorothy and primary knowledge of the powerful magical artifacts existing worldwide – the ÄRMs.

After aiding Dorothy on her ÄRM hunt, Ginta's forfeited the ownership of the dormant legendary ÄRM Babbo, a sentient weapon that is just as vexing as it is fabled. Ginta's and Babbo's bickering eventually leads to their newly founded company crumbling, landing Babbo in the hands of two ÄRM thief con men, Moku and Chapu. However their identity is quickly exposed, and after Ginta forcibly reclaims Babbo, the two reconcile.

Ginta's traveling leads him to the house of Jack, a father-orphaned farmer of Ginta's age living with his hospitable mom. They befriend each other after the two vagrants help him outfight the Rogelu brothers, two werewolves terrorizing Jack's farming, and Jack decides to accompany Ginta on his way to find a way back to Earth.

The trio arrives at Pezu, a small town where Jack does his trading. As their efforts to search out the occult clown Dimension ÄRM turn fruitless, more trouble's to come: Ginta's again robbed of Babbo by the Stanley bandit. When the boy fights to recover his ÄRM, one unlikely hand of help extends from Alviss, a mysterious yet hostile boy introducing himself as the one who summoned Ginta to MÄR-Heaven using the "Monban Piero" clown ÄRM.

Alviss’ arrival brings a dark secret to light: the existence of a rebellious military faction known as the Chess Pieces army, which 6 years ago came within an ace of conquering MÄR-Heaven before it was quelled by the world's guardians, the Cross Guard soldiers; and the need to dispose of Babbo due to its gory history of massacring people alongside the Chess un-dead commander, Phantom. Much persuasion, and even retaliation (though vain) is needed from Ginta to change Alviss' mind, including a promise to get stronger. Meanwhile, in a lightning-zapped graveyard, one bevy of masked warriors salutes a man, seemingly resurrected from inside his tomb, whom they addresses as 'no.1 Knight Phantom'.

Soon after the confrontation with Alviss, Ginta & co. encounter Edward, a small dog-man introducing himself as the custodian of Snow, a princess currently fleeing from her stepmother queen, an insatiable woman who, out of desire for the world's throne, makes attempts on her stepdaughter's life to reign over the entire kingdom. On Edward's request to rescue the princess, who at the moment is dying inside a frosted palace, Ginta discovers that the girl bears an exact resemblance to his Earth friend Koyuki, and the minions Ian and Loco that the queen sends after the princess turn out to be none others than Chess Pieces.

Ginta's clash with one of the two Chess Pieces, Ian, tends to favour the latter as Ginta's far too inexperienced and unequipped for the use of Babbo. As the situation necessitates it, Edward reverts to his second form, Alan, a man with yet to be revealed identity but much dreaded by the Chess members, buying Ginta enough time to unfreezes Snow and (accidentally) exchanges a kiss with her. In the middle of the confusion, Halloween, a Knight of the Chess Pieces – an acquaintance with whom Alan stays in discordance – arrives to summon his subordinates back for the Chess Pieces' official issuing of war declaration against MÄR-Heaven.

Phantom, the ‘no.1 Knight’ zombie from the resurrection assembles all Chess Pieces warriors in the hall of a levitating castle and loses no time raising his men's esprit de corps with the long-awaited declaration of the 2nd Marchen war. At the same time, Ginta's gang meets with Dorothy; and Alan sends all four of them into the training dimension of "Training Gate" (Shuuren no mon) for a quick fighting coaching, knowing time's running out.

Inside the Gates, Ginta and Snow, Dorothy and Jack, each group greets their respective training navigator Meriro (a soft-spoken, cute nekomimi) and Bumolu (a dumpy and foul-mouthed bearwoman) and enters their training session: Ginta learns of the truth behind Babbo's fame as a legendary ÄRM – the ability to metamorphose into 8 powerful versions, and Jack gets his incapable scoop ÄRM upgraded with Dorothy's magic stones. Outside, Alan accosts the aforementioned Alviss, whom he recognises as a fellow Cross Guard member 6 years ago, though was a child at that time.

As sunset dawns, the Chess Pieces soldiers, with Phantom assuming their command, grace their returned heyday by showering the whole MÄR-Heaven in a mass blood-bath. The emergency transmitted by Cross Guard troops throughout the world reaches Alan and Alviss as they discuss whether Ginta's potential can outdo the late Cross Guard general (also one man from Earth world), and Alviss departs in a hurry after scowling Alan for remaining on his post beside the Training Gate when MÄR-Heaven's in dire need of his help.

Just before the 180-day deadline reaches its end, Ian uncovers their training spot and battles a physically deteriorated Alan to advance on Ginta's dimension. The trainees finish their session just in time to fend the Rook off, and Ginta settles their duel with a win, using v.2 of Babbo Bubble Launcher.

Now with Dorothy on their side, there lacks two more members to incorporate team MÄR which, according to Snow, will defend MÄR-Heaven in the Cross Guard's stead. On their way to Hild continent, Ginta & co. are ambushed by Luberia, MÄR-Heaven's most prestigious thief guild. Therefrom they meet and ally with Luberia's captain, Nanashi, whom turns out to be seeking after a man from Chess responsible for the assault at Luberia's base fort just before the war. In the faraway Lestava castle, the news of Ian's punishment for disobedience to command reaches him, his girlfriend Gido (also his companion on the search for Ginta) is to be executed in his place. Meanwhile on Earth, Ginta's mother is depressed about his absence, but Koyuki comes over daily to relieve her with the experience she has via her counterpart, Snow.

Now accompanied by Nanashi, MÄR arrives in Vestry, a coastal village wrecked after a Chess' carnage and divides their numbers to help the people and exile the Chess away from that part of the continent. Ginta later befriends Tom, a (self-claimed) native young boy habitué of the haunted Vestry cave while on the other side of the underground route, Dorothy & Nanashi encounters a Chess Bishops-ranked homicidal brute, Orco, and Dorothy's for the first time overawed at Nanashi's prowess.

Ginta's 2nd Chess adversary introduces himself as another Bishop-ranked psycho, Girom. Granting the request of the cave ghosts, Ginta resorts to his powerful v.3 Babbo Guardian ÄRM, Gargoyle, and defeats Girom, blasts the cave's blockade, setting the ghost free. In return, they presents him a key and a magic stone as a token of gratitude. Observing the scene, Tom switches off his façade and reverts to be the genuine Phantom, killing the loser Orco as he leaves.

A filler episode. Ginta's team runs into John Peach, a loudmouthed boy claiming himself to be the hero that shall save MÄR-Heaven from under the Chess Pieces claws. He steals (thinking he's earned it) gold from some thieves who happens to have a strong spider ÄRM (who he later gets by accident). Peach, thinking he's the hero, challenges Ginta to a match which Snow later says will be a race. Stupid things happen, and Dorothy later explains that the spider ÄRM is really rare since no one uses it, because the spider is uncontrollable and to stop it, it has to eat the user. Peach activates it, and much to his avail, almost gets eaten by it. Ginta saves the day, and Peach says he'll get stronger.

In Vestry and throughout the world of MÄR-Heaven, the Chess’ announcement of the War Game rings like death knell, gathering all its adversaries to Reginrave castle, stage of the preliminary round. However, aside from Ginta's MÄR team and Alviss of Cross Guard, none of the salvaged fighters gets out of it alive.

1st Round, 1st battle, Reginrave castle stage, Alviss wins his first victory against a Rook named Leno Rodokin. His Cross Guard past as a child is brought into light, including his fatal first meeting with Phantom, which has resulted him his cursed blemish, the Zombie Tattoo.

1st Round, 2nd battle, Reginrave castle stage, Jack against Leno's Rook sister Pano Rodokin. The battle ends a comical loss on Jack's part.

1st Round,3rd battle, Reginrave castle stage, Ginta vs. Garon Rodokin, the Bishop father of the previous Rook siblings. The utilization of his invincible Guardian Gargoyle brings about Garon's ultimate defeat.

As the meaning of resemblance between Ginta and the Cross Guard former captain Danna dawns on him, Gaira summons him and Jack back to the Training Gate. Meanwhile, Ian approaches Phantom and requests the same, Ginta's true capacity has precipitated the time he carries out his vow: to kill Ginta and Gido's punishment executor.

2nd Round, 1st battle, desert stage, Snow of MÄR and Fuugi of Chess Pieces duel. Snow's giant Snowman "Yuki-chan" slams quickly crush Fugi and his geographically advantageous Wind Arm.

2nd Round, 2nd battle, desert stage, Nanashi vs. Loco. The Rook's mastery of Darkness ÄRMs corners Nanashi (in its physical literality) into a paralytic position. Though he manages to beat his way out of it without killing the girl, the excruciating pain from her voodoo tools takes it toll and he loses.

2nd Round, 3rd battle, desert stage, Dorothy against Maira. Ignorant of his opponent's magic kingdom nationality and her inhumane notoriety, the Bishop challenges Dorothy with his amoeba Guardian Vacua, only to be devoured altogether by her Guardian dog Toto.

On the night before the 3rd Battle, Ginta runs into "Tom", who with the Chess Pieces hot at his heels, beseeches the boy's help. However the hunter (who turns out to be Peta) outwits both, and kills "Tom" right in front of Ginta. Leaving the boy with his wrath provoked, Phantom returns from his framed "death" with his head high; Ginta's bound to give all out against the Chess in the future, given they've murdered a 'friend' he's promised protection.

3rd Round, 1st battle, volcano stage, Alan wakes from his slumber inside Edward to combat the Rook Alibaba, who deliberately spars with Cross Guard's 2nd-in-command to ascend to Knight class. With little effort, he obliterates the presumptuous tyro's Guardian Genie's Lamp, showing him his place, and casually tosses him into the volcano for his disrespect.

3rd Round, 2nd battle, volcano stage, Jack vs. Pano rematch. Jack's continuous trainings come to fruition; his hallucinatory toadstools triumph over her primal Weapon ÄRM, and inadvertently earn him her affection in the process.

3rd Round, 3rd battle, volcano stage, Snow vs. the Bishop pirate Mr.Hook. Though she fights with courage, the heated battlefield gains Mr. Hook an upper hand against her ice-elemental ÄRMs, and her drastically halved magic power eventually fails her.

3rd Battle, 4th round, volcano stage, Ginta against Kannochi. The Bishop's shrewd deployment of his Body Candle ÄRM lands Ginta in a deadly crisis, but the boy's timing summon of his Holy Guardian Alice quickly turns the table, inflicting the curse back upon Kannochi in his place.

3rd Battle, 5th round, volcano stage, Alviss spars with the adolescent - albeit proficient in the field of explosive Nature ÄRM - Rolan of the Knights, only to find out that while he's not the only one bearing the Tattoo curse of immortality, he appears to be the unique to harbor grudge against it. That shock from which he has no time to recover and Rolan's ceaseless blows simultaneously exhausts Alviss of magic power, beating him hors de combat.

MÄR's victorious choir is soon to be silenced as they return to the Reginrave castle base just to find Phantom and his Zodiac Knights ready on the welcome spot. Ginta uses Alice, Babbo's Holy ÄRM form, to break Edward and Alan's curse. Unfortunately, Alice cannot cure Alviss' Zombie Tattoo.

As the Knights' official introduction heralds their participation in incoming battles, all member of MÄR (with exclusion to Snow, who needs to rest due to her being weakened at her last fight (although she convinces Alan to let her go later anyway), and the newly Edward-split Alan) are to again hone their skills in the Shadowman "Shadow fight" of the Training Gate.