In the process of extracting oil at the drilling station in Gambridge, the Core Force receives a shock and the sealed Absolute Evil, Rout, wakes up. This accident creates the Mix Zone between Gambridge and Atreia and it is an omen that the world is going to collapse! The elders of Atreia send out the Master Hench to Gambridge to find four Mix Masters to save the world from this crisis.

While the Mix Masters are trying to change Ditt's mind, Ditt's partner Chichi thinks that it's all his fault. Ditt goes to the Atreia Forest alone to find the legendary Master Hench, Pachi, but gets caught by Babel instead. Ditt remembers his duty after saving Chichi and swears to save the world as a Mix Master.

The Mix Masters visit the zoo and give Master Hench a tour of Gamebridge. But Eva suddenly appears at the zoo and attacks them. She turns Sea Turtle Ally, Aring's closest friend, into a monster! Aring resists Eva with all her might and Ditt is touched by her devotion so he decides to try Extreme Fusion with her. Dinoking and Goldhawk successfully combine their powers for the first time.

Mir finds out that Ray's birthday is coming up soon. So Mir plans to throw a surprise birthday party at the amusement park with the Mix Masters and Master Hench. But Ray doesn't feel good about his birthday because his brother, who he always felt inferior to, died that same day. The Mix Masters get split up at the amusement park and Babel makes the most of his chance to attack the Mix Masters.

Moreen is born with the ability to predict the future. People ostracize her because they think she is cursed. But Moreen always stays cheerful and lives her life as best as she can. The Mix Masters find out about her past and help her become Top Master to complete their Mix Combination in their battle against Eva.

The Mix Masters take the Master Hench to Atreia to celebrate their graduation from Hench School. Ditt gets fooled by a fake Pachi that Eva made. A monch attacks him and chases him to the edge of a cliff. Meanwhile, Wolfman teaches a special training session for disqualified Hench. During the training session, Chichi senses that Ditt is in trouble.

Babel devises a scheme to create chaos in Gamebridge town by convincing Ditt's father to spread a contaminated fleshy plant. Ditt's father becomes a millionaire by selling Dayougi plants. He turns into a different man. Ditt finds out the truth and defeats Mandramonch, a dark mixed fleshy plant beast. But Ditt is still unable to vent his rage toward Babel.

After Ditt checks out the Red Temple, the Mix Masters have a meeting with the elders of Atreia. At the meeting, they find out the Red Temple is actually the main enemy base. So they set off on an adventure to find it. However, no one has ever opened the gate in the Mix Zone that leads to the Red Temple before.

The Mix Masters finally enter the "Door That Cannot Be Opened", but they find a steep cliff and a narrow bridge on the other side that leads to a dark forest. They enter the dark forest and accept the hospitality of Narsia, a butterfly Hench. But it's a trap and they end up trapped in the Insect Village jail.

The Mix Masters find their way to Man's Cave with Eva's map. But a suspicious beggar by the name of Kayon follows them. After a long journey, they finally arrive at a large train station. When they finally get inside the station, Babel stops them and tries to mix an earthworm and a cable car!

The entrance to the Red Temple is a twisted maze, making it hard to get in. Ditt tries to enter and falls into a trap. Chichi and Kayon get separated from the team and wander around in the maze for a while. Each of them solves a question to open the gate and finally end up back together at the final gate. The Mix Masters then defeat the Armor Knight to go deeper into the Red Temple!

The Mix Masters enter the boiler room that supplies energy to the Red Temple. Aring and Ray turn into stone after being deceived by the Hench that guard the boiler room. However, Ditt and Moreen find the passage that connects it to the Red Temple. The Mix Masters defeat Babel's Chainmon and finally enter the Red Knight's chamber!

The Mix Masters just barely arrive at the Red Knight's chamber. But when they get there, their Mix Launchers don't work! There is nothing the Mix Masters can do, so Kayon transfers to defeat Babel! Kayon reveals the truth about the Red Knight and the secret to the Red Temple.

The Red Knight who used to be a Mix Master gets completely dominated by Core Force, and the Red Temple gets transformed into Amoknight. The battle between those two and the Mix Masters gets more violent. As the battle rages, Amoknight threatens Ditt, Ray, and Aring's Mix Launcher power. The Mix Masters combine their powers to successfully Mix into a strong Delta Warrior and defeat Amoknight.

Things are peaceful in Gamebridge, and Gamebridge School is holding a school arts festival. Ditt's class prepares for a play: Snow White. Baba, the worst-behaved student in Ditt's class, bullies his classmates into giving him the leading role and letting him direct the others when the teacher is busy. But after defeating the Red Knight as a Mix Master, Ditt is not so timid anymore!

Gamebridge School is conducting psychoanalysis tests and Ditt accidentally puts what he thinks are the correct answers in the wrong place for every question. He gets sent off to Outcast Camp and meets Juho. Blue Fox hands the Black Mix Launcher to change Juho into a Black Mix Master. But when his hedgehog gets changed into a monch because of a disturbance, the Mix Masters come to the rescue.

Tomo is always being smothered by his mother who keeps a close watch on him. He befriends Moreen who notices his artistic talents. He enters an art competition and wins, but his mother isn't pleased. She tries to send Tomo away to study abroad. He becomes confused and upset. The evil Blue Fox takes advantage of his confusion, and transforms him into a Dark Mix Master.

Ray's childhood friend Yuna transfers to Gamebridge School. Yuna wants Ray all to herself, so she gets jealous of his friends. The Blue Fox uses her feelings to turn her into a Black Mix Master. Ray assumes the Top Master position to rescue Yuna. In the end, Ray lets her know his real feelings: he thinks of her as his good childhood friend.

This is the story of how the Black Mix Launcher was born. Blue Fox made the Black Mix Launcher with the remains of the Red Temple after the Mix Masters defeated the Red Knight. Blue Fox, disguised as a store clerk, gave the Black Mix Launcher to Youring, Aring's little cousin, to find out what the Black Mix Launcher could do.

Jina is stressed out because she thinks her face is unattractive, even though she is an awesome athlete. Blue Fox gets on Jina's nerves, takes advantage of her insecurity about her looks, and gives her the Dark Force Makeup Box. Jina fools everyone with her new Dark Force makeup, but Aring senses something is wrong.

On the day of the Gamebridge School trip, Hiro gets scared and sees ghosts even though other students can't. The Blue Fox exploits his fears to turn him into a Dark Mix Master and causes him to create a disturbance on the school trip. The Mix Masters combine their powers to purify Hiro.

Ditt cheats on his final exam in order to get out of having to attend supplementary lessons, but he ends up scoring at the top of the class and is selected to participate in a contest as the Gamebridge School's representative. Mino is the representative for River Town School and feels the pressure to win. Blue Fox uses his stress to turn him into a Dark Mix Master.

Wolfman, one of the members of council of elders in Atreia, starts an investigation into the mystery of the appearances of Dark Mix Masters in Gamebridge Town. Wolfman successfully infiltrates Blue Fox's hideout, but loses his memory. He makes a deal with the Dark Launcher and ends up fighting the Mix Masters! After being purified, Grandpung helps Wolfman get his memory back.

Luna is always jealous of the attention her twin sister Sunny gets from their mother. Blue Fox convinces Luna that her mother actually likes her sister more than her and turns her into a Dark Mix Master. Ray understands Luna's desire to be recognized by her parents, so he tries to save her. In the end, Luna gets purified and resolves her misunderstandings with her mother.

The Mix Masters cross the Mix Zone that Wolfman discovered and arrive at Blue Fox's hideout. They fight Lofa, the Monch that guards Blue Fox's place, and Blue Fox joins the fight. Ditt, Aring, and Moreen manage to force Blue Fox to bounce back out of the Mix Launcher. But Ray's sense of guilt about his brother's death changes the Core Force formula and turns him into a Dark Mix Master.

Dark Mix Master Ray takes the Mix Masters to the Island in the sky Minus Ziggurat. They are in danger of losing their Core Force. Ray falls for Blue Fox's trick and thinks that he might be able to bring his dead brother back to life. He fights Ditt, Aring, and Moreen. But in the end, he feels the warmth of his friends' true hearts and frees himself from the dark Core Force.

After Ray becomes contaminated by the Dark Core Force, questions about his qualifications to be a Mix Master cause controversy in Atreia. In the meantime, Blue Fox secretly steals some Core Force and throws it into the Mix Zone, but part of the Core Force doesn't get collected. Because of this, Gamebridge and Atreia actually start mixing together.

After a Mix Zone is created between Gamebridge and Atreia, the two worlds fall into chaos because of many sudden unexpected changes. In the meantime, Moreen finds a fairy tale book that her mother often read from when she was little. A lady with silver hair suddenly appears in Gamebridge, and Moreen has a feeling that it is her mother.

The Lady with Silver Hair drags Moreen to the third space. Moreen tries to find out if the lady is her biological mother, but the lady won't give her a straight answer. Meanwhile, the Mix Masters try to bring the Hench that came to Gamebridge through the Mix Zone back to Atreia. But they are mistaken for terrorists. Moreen senses that her friends are in danger and tries to return to Gamebridge.

After the appearance of the lady with silver hair, Moreen keeps wondering who her real mother is. She finds out that her mother disappeared when Energy R1 exploded in the lab. Meanwhile, the lady with silver hair mixes a Monch and disappears. As the Mix Masters are defeating the monster, they are caught on TV and they become instant stars.

Because reporters ran a story with a picture of what they said might be Moreen's real mother, people start saying that the lady with silver hair might indeed be Moreen's real mother. The Mix Masters fight the lady with silver hair who wants to abduct Moreen. After the fight Hench Hammerlong gets purified and tells them that Moreen's real mother had another child named Root.

Moreen's stepmother let the Mix Masters know that Root is R1, a type of energy with personality. Meanwhile, the appearance of Mix Zones everywhere throws Gamebridge and Atreia into chaos. Moreen fights back against Silver and wins thanks to support from her stepmother and the Mix Masters. Silver finally disappears and Root reveals himself thanks to a magic wand.

The Challenge Group send a robot to explore the Mix Zone and find out the structure of the connection between Gamebridge and Atreia. The Mix Masters realize this place is actually Root's hideout and go there to find him. Root and Battle figure out that the Mix Masters have discovered their hideout and run away to Gamebridge.

The Mix Masters enter Root's hideout one more time. When they do, characters from the fairy tale book, Foxy and Slow Red Knight, appear in front of them. The flying fairy tale book leads the Mix Masters into Root's Crystal Chamber. Root uses dark powers to dark mix Fox Knight. Root captures Ditt's soul in his crystal ball and steals his body.

Root kicks the Mix Masters out of Root's World and asks Ditt to take away his spirit completely. He tries to convince Ditt to choose his future after Root shows him a pathetic vision of what might happen. But Ditt chooses his own future even if it looks pathetic. Meanwhile, the Mix Masters use the Mix Launcher to find Ditt's location. They fight the gatekeeper sphinx to save him!

The Mix Masters find a vending machine that has capsules in it. They struggle to take out the crystal ball with Ditt in it and end up fighting the Dark Dinoking that is controlled by Root. Root tries to get rid of Ditt out of anger, but Moreen blocks his attack. Moreen falls down after getting hit. Root takes her and disappears.

The Mix Masters follow Root to his hideout to save Moreen. The Mix Masters end up using all their Core Force in the ensuing battle, but thanks to Pazzi, they are able to release the sealed Core Force inside the Ziggurat which collapses Root's world. They save Moreen and escape to Gamebridge.

Root gets angry at the Mix Masters, so he follows them to Gamebridge to destroy it. The Mix Masters decide to turn themselves into their Core Force to boost the power of their Mix Launchers. Fighters from Gamebridge and Atreia use their Core Force to combine their powers and create the Ultimate Guardian for the final battle.

The Mix Masters defeat Root with the Ultimate Guardian. The world finds peace at last. Root tried to create the world in his own image, but finally realizes the story that he knew was only half of the fairy tale. After Root goes back to nature, Core Force spreads around the world, allowing the Mix Masters to return to their normal lives... But the world soon faces another crisis.