Genki is a young boy with an ordinary, dull life. That is, until he gets a new game in the mail. He soon gets pulled in and must now fend for himself within the game. He soon comes across two friends, Suezo and Holly. But, will they be able to stop the terrible monster, Moo?

Genki, Mocchi, Holly, and Suezo continue on their trek. Genki is concerned, however, that Mocchi is becoming a softy, so he decides to leave him with an elderly couple they meet outside of a town. Genki wants Mocchi to stay with them, but Mocchi refuses and shows his friendship toward Genki by helping him defeat the Black Dinos.

Genki and friends come across an "enigma", a Golem that does not like to fight. They invite him to join their quest, but when Moo's troops threaten the Golem's “Garden of Lost Disks”, they discover a terrible secret about him!

Genki and his friends encounter Alan, a young boy who is strict and cruel to his pet Worm. When he tries to ally with agents of Moo, however, he learns that loyalty is something that is given and not taken.

Genki and his friends come across a group of bandits in the desert, led by Tiger of the Wind. He steals the Magic Stone, but the Baddies turn all of his friends into Mystery Disks and injure him. When Genki and his friends save him, he helps them defeat Captain Dino and then joins them.

Genki and his friends reach a town with a giant coliseum! Tiger battles Hare, who cheats his way to a victory. Genki and the others soon forgive him and Hare offers to buy them dinner and a place to stay the night. In the morning, Hare runs off and leaves them the bill, but Tiger catches up and makes him pay. Hare apologizes, and joins the group.

Genki and his friends come across a beautiful valley with a small village at the foot of a dam. When Moo's troops damage the dam, Genki and the monsters must work together to save the town from utter disaster!

Holly's past is finally revealed! She shares her story with the gang on a miserable, rainy day. She tells of how she came to be on the quest for the Phoenix with Genki and the others.

Genki and his friends continue their journey, and find a huge canyon, as well as a beat-up airplane. They take the plane, but has Genki been double-crossed by the pilot? The group must fend off the evil Kuro in order to get out of this predicament.

Genki and friends arrive in Heaven Canyon via the iron bird. In the canyon are humans mining “mystery disks” under the oppression of Moo. Are Genki and his friends strong enough to defeat them and free the imprisoned humans?

After scaling a cliff, Genki and Mocchi must free their captured comrades and find a way to defeat Clay, Pixie, and Big Blue!

In search of a mysterious disk, Monol tells of a great story from the past.

Genki and friends meet paths with the infamous Moo. Will they be strong enough to defeat him?

The Searchers, aided by the Pirate Dragons, infiltrate Moo's castle. Moo tells of how he left the village and was infused with Holly's father. He also gives Holly his dagger, which was Holly's father's, to prove it. Then Genki and his friends save her, with the help of Pixie.

The Searchers arrive to the ocean, and encounter Horn, the self-proclaimed righteous pirate. They try to get him to give them a ride across the ocean, and fight Gali's Zuum troops at the same time.

On the high seas, the team is attacked by Moo's Zillas and their leader, Gooji. Unless Golem can overcome his fear of the water, this may be the end for Holly!

After trying a shortcut, the team becomes trapped in a mysterious underground cave. Will they be able to find their way out when Moo's sinister Joker and the Evil Hares are there to wreak magic havoc?

The Searchers discover an ancient city, perfectly preserved by Hengers. But, the robot caretakers are programmed to prevent anyone from entering it! When the Hengers take Holly's pendant, Genki and his friends must trust a malfunctioning Henger, who was banished from the city because of his free will, to find a way inside.

Suezo has always been happy to let others do the fighting for him. But, his friends have begun to take him for granted, and when Hare points out that he has no Special Attack, Suezo takes the criticism pretty hard. Genki begins to try and train him, but does Suezo have the courage it takes to show what he can really do?

Pixie returns, and helps Genki in a battle against a group of Scale Jells. But she and Genki become separated from the others, and when Pixie gets injured, she finds she must rely on Genki to survive. At first, she is embarrassed and angry. But Genki's compassion begins to wear away at the barrier of hatred she has built around herself.

The Searchers finally confront Gali, the second of Moo's Big Four. Gali is both charming and clever, and manages to trap Genki and the others in a pit. But Mocchi escapes the trap, and the young monster must fight, alone, in order to save his friends.

The Searchers are attacked by the Black Worms, who are under Gray Wolf's command. Tiger must save the group and come over the realization that he must be the one to defeat his brother.

While wandering through a hude, dark forest, the Searchers are captured by a group of Moks, led by their captain, a dark Mok named Ebony. Mocchi manages to escape, and befriends a Ducken, who had been hiding in the forest from the Moks. Can Mocchi save Genki and the others or will his efforts get his new friend captured as well?

Genki and his friends come across a trio of Centaurs, proud warriors who serve Moo, but have a code of honor of their own. They challenge the Searchers to a tournament, but there is a squad of Salamanders in the area as well, and they don't want the Centaur to have the glory of Genki's capture.

The Searchers come across a small, quiet lake in the forest. They decide to restock their food supplies with fish. However, the lake has another inhabitant, an Undine. Golem falls in love with the beautiful water spirit, but she turns out to be a servant of Moo. Will he be able to defeat her?

While running from a squad of creatures called JaggerNauts, Genki and the others stumble across a factory. The JaggerNauts follow them into the factory, and they battle. However, an android, Melcarba, is still lying dormant in the factory for millions of years and kills all of the JaggerNauts. Then it turns on the Searchers, and they have to use the lightning storm to shut down the derranged cyborg.

Genki and the group enter Naga's territory, which is also the Color Pandoras' forests. Naga sends Stone Dragon to destroy them. Meanwhile, the group falls into one of the Color Pandora's traps. They eventually understand each other, and work together to trap Stone Dragon. But when Stone Dragon breaks free, Color Pandora then turns him into a Lost Disc...

Genki and the group meet up with Jim and his Eared Mew at the Yellow River. They battle Baddies as they cross the river. Genki is angry at Jim, who thinks that he is just a kid, but sees that Genki is a strong person when he saves him.

Genki and the gang resurrect Bossy. The Apes worship Bossy, because he finds them food and shelter. But the Rock Apes steal him for the same purposes, and Genki's gang collaborates so both tribes are equal among Bossy's rule.

Genki and the gang locate an abandoned amusement park that is the remain of an ancient civilization. They all explore, until the Kuros kidnap Mocchi. They beat the Kuros, but Pixie comes to tell them that Moo found his body.

The gang meets up with Niton, a snail-like creature who is a merchant. He sells them second-rate quality items and a fake mystery disc for Holly's dagger. Infuriated, they go to find him, but the Jells trap them on the beach and bury them. But the tide is coming in fast. Holly begs Niton to help, and he finally comes to his senses and does what is right. He digs them out and gives them a refund.

Naga sends the Tainted Cat Brothers to destroy Genki and his friends. Mocchi and Genki are separated from the group, and meet with the Tainted Cat Brothers' old mentor, Kato. Kato trains Genki and Mocchi, and together the two help the Tainted Cat Brothers realize that they were wrong to turn against their mentor.

Naga sends his most powerful warrior, Bajarl, to destroy Genki and the others. Bajarl traps them in his jar, and only Holly and Mocchi escape. Holly then stumbles onto a ghost town that was wiped out by Bajarl. Holly reads the mayor's diary, realizing that the mayor rigged a huge rock formation above the town with explosives. She blows up the rock, trapping Bajarl and saving her friends.

The gang infiltrates Naga's headquarters to take out the last of the Big Bad four!

Moo is finally merged with his body and immediately seeks out Genki's group. They are currently traveling over a mountain, and they come across a sleepy village. The village doesn't answer when they ask to stay in, because it is "Ogre Day" in the village, where an ogre comes and steals children. A little girl, Eve, leaves her house on during the night to seek out the mystic god who will kill the ogre, but she finds Moo, and he holds her inside an energy bubble. Moo confronts the gang, and his overwhelming offense power squashes them. But, when it looks like the end, the sun arises. Moo cannot stand the light, and flees. Eve is rescued.

Genki and the monsters celebrate Holly's birthday.

Moo orders General Durahan to destroy Genki and his group. Durahan sends End Bringer, who is stronger than the group. But the group's courage fuels them to destroy End Bringer.

Durahan sends Chariot and a pack of Salamanders to destroy the group. The Salamanders are reluctant to follow the group into the forest, because a monster is rumored to live there. Chariot orders them to kill the group, regardless of some rumor. The gang finds Baku, who likes Genki. Genki resembles his owner, who was killed when Chariot destroyed Baku's village. Baku turns Chariot into a lost disc, but Baku is changed into a lost disc also.

Genki and the group come across ruins, which an archaeologist, Colt, is excavating. She tells that the ruins are the remains of the "Pendant" civilization. This civilization has the same crest as the Baddies. Anyhow, Durahan sends Metal Jell and a squadron of Knight Mocchi to destroy the group. Genki and the others trap the Baddies in a moster-making factory in the ruins. The factory experiences an electric surge, and explodes with the Baddies inside.

The team takes a break in a meadow, and Tiger goes to look for food. While he is gone, Jagd Hound attacks. Tiger chases him, because Jagd Hound was not a Baddie. Tiger learns that Lilim kidnapped a baby Jagd Hound swore to protect, and the only way Jagd Hound would get it back was if he destroyed Genki's group. So Tiger and Jagd Hound fake Tiger's death with an Evil Hare lost disc to trick Lilim, and her plot is foiled.

Durahan unleashes a squadron of Astros to destroy Genki and the team. They lose the Astros in the ruins of a spaceship, and Captain Astro finds them and tells of how the people of Vangea tortured them, and he wants revenge on all humans. He does not realize that not all humans are evil until he falls down a waterfall, and Genki tries to save him. Astro becomes a lost disc.

Durahan sends Renocraft to destroy the group, but they succeed in turning him into a lost disc.

Captain Weed realizes that the Magic Stone is needed to perfect his body. He tells Durahan to get it. Durahan wants it for himself to overthrow Moo. Durahan sends the Gangsters, which are self-reassembling robots. Lilim gets the Magic Stone before Weed does, and goes to give it to Durahan.

When Lilim returns, she tells Durahan that she would rather give the Magic Stone to Moo. All of Durahan's forces have turned on him, and to make matters worse, Genki and his friends teleport to Durahan's warship. Lilim rigs it to explode, and she gets away with the Magic Stone. Genki and his friends confront Durahan and defeat him. Then they escape from the Iron Bird before it explodes, with Durahan onboard.

The group travels north, and comes across a village of Jill. Jill tells them of the legend of Cinderbird, who changed the evil Skullcapt into a regular Jill. Jill decides that Genki and his friends have true souls of goodness, and decide to show them the Phoenix, which is encased in a giant ice cube. But Moo comes, fully reenergized. Genki and the others attempt to lead Moo away from the Phoenix.

Gray Wolf challenges his brother, Tiger of the Wind, to a one to one duel to settle things. Who will be the victor?

Genki and the others attempt to lead Moo away from the Phoenix, when Pixie and an army of the Pirate Dragon army, led by Vulcan. Pixie is seriously hurt while fighting. But instead of finishing them off, Moo goes berserk. His mind is strangled by the evil fury of Moo's soul. Meanwhile, Pixie is in danger of becoming a lost disc. Big Blue decides to fuse with Pixie to save her, even though he ceases to exist. They fuse into Granitee. Holly realizes that in order to summon the Phoenix's soul, they might have to fuse monsters that the Phoenix's soul was reincarnated into.

Moo is so berserk that he has even started to destroy the Baddie armies. He then travels to Mt. Kyrus to destroy the volcano. The magma, Monol tells them, will cause a chain reaction inside the planet and cause a catastrophic earthquake that will destroy the planet. Monol also says that the Phoenix's soul was split into five subdivisions and fused with five mystery discs. He says that the monsters are Suezo, Mocchi, Tiger, Golem, and Hare. The five fuse into the Phoenix. Both the Phoenix and Moo are destroyed in the battle, and Genki is shunted back to his own time.

A year has passed since the final battle with Moo, Genki still cannot forget his friends. Suddenly he is led by an image of Mocchi to a deserted shop with a Monster Rancher game disc. Playing the disc he sees his friends quest to defeat Moo unfolds before him and saw what happened in his absence. After the battle, the gang is seperated. After finding and unlocking Mocchi from his Mystery Disc, Holly and Mocchi embarked on a quest to reunite the gang. They found a Mystery Disc containing Moo and Holly's father. Baddies reappear to claim the disc and the duo are in danger with Mocchi losing all his fighting abilities when he was turned into a Mystery Disc after the final battle with Moo. Also, a mysterious enemy seems to be behind the baddies.

Holly is determined to free his father from the Disc and trap Moo inside. The three enters a city to eat and while they are there, they saw Poritoka and Most in the Legend Cup competition. They were shocked at Poritoka's amazing fighting abilities but even more surprised when they saw the Magic Stone on the Winner's Plate.

Genki thinks that the Magic Stone can help to release Holly's father. They were told that defending champions Poritoka and Most only appears in the Legend Cup. Genki and Mocchi decided to enter and win the Magic Stone for Holly. They also got reunited with some old friends.

Genki and Mocchi take part in the first of six competition that leads to the Legend Cup. Not only was the title at stake, a Mystery Disc containing Tiger is also on the line!

Although Mocchi lost most of his fighting abilities, Genki's training allows Mocchi to make it into the final of the Rookie Cup. There Mocchi met an opponent of great skill, how can Mocchi win against an opponent that is way beyond the rookie level? Is this opponent really another competitor or is there something else to it?

The gang runs into Hare at an orchard and finds out that he has been living with Tama who saved Hare after the battle with Moo. Seeing that they are on such good terms, the gang cannot bear to break them apart. Leaving Hare behind, the run into Zerbasaurians that are sent by General Durahan. With Holly held hostage; Hare comes at the nick of time to save the day. In the end, Tama makes a tough decision to let Hare go.

While Mocchi is searching for food, he chance upon the Wondar Brothers. The younger Wondar is a huge Hare Type monster with immense strength while the elder Wondar is good with his brains. Mocchi brought them and their gift of gigantic potatoes back to the gang. Just as they were about to become good friends, the elder Wondar revealed that their goals clash, for he wants his younger brother to become the strongest monster there is!

Tiger wants to make his debut at the Mandy Cup but everyone is worried that he won't be able to do it without his abilities (which he has forgotten). Genki tried to teach Tiger some defensive moves but Tiger insists on continue practicing alone to receive his abilities. So, Genki and Tiger broke out into a fight and when they enter for the competition the next day, Tiger refuses to be coached by Genki.

The competition format is 2 monsters per team and 1 on 1 battles. If there is a draw, a 1 on 1 Sudden Death round will be held determine the winner. Despite not having their more powerful moves, Tiger and Mocchi were able to win their rounds and made it to the finals.

The gang got interested in Hare's little baggage but Hare refuses to show them. Then, a small Dinosaur came and stole Hare's baggage! The gang gives chase and found that the Dinosaur is an orphan living under the care of Fairy Hare, one of Hare's long lost friends.

Fed up with their failures, General Durahan sends out his Shelly Gabus to deal with the gang. The Gabus caught up with the gang who found themselves on a deserted sea platform. After an intense battle, the Mystery Disc dropped into the ocean.

As Mocchi and Genki searched, they encounter Professor Garnish's submarine. Garnish thought they are after his dream treasure (which is actually some sunken treasure of a pirate ship) and chased them away with his cannon. The gang came back after realizing that the only way to get the Mystery Disc back is to make peace and get Garnish to let them use the submarine.

In this competition (3 rounds, 1 on 1), Mocchi must enter with two other monsters in the list that is designated by the IMA. Guess what? Only Golem and Suezo qualify! While Golem is fine, Suezo is terrified. Furthermore, there is only one other team in this championship! So the decided to win the first two rounds so Suezo does not have to fight!

As they get ready, Suezo found himself helping a kid, Furred Suezo (to show him what bravery is all about) from another bunch of Suezo bullies who took his trading cards. Suezo decided to stand up for him and managed to get back the rare autographed Poritoka card but in the end the Suezo gang caught up and they were both beaten up really badly.

The gang tries to cross the marshlands but have problems with getting a cheap taxi. In the end they took Sandra's offer of 700 gold. The first half of the journey was a roller coaster ride with Golem barely hanging on! Halfway through the marshlands, Sandra suddenly stops and tells them that she is going back!

It turns out that she is trying to rip them off since she knows they are loaded for their victory in the last competition is all over the news. She asks for 3000 more gold and they broke out into an argument. After failing to reach an agreement, Sandra threatens to leave them in the marshland. The gang decided to perform to get a price cut and in the end managed to resolve it for another 1000 gold against the backdrop of going deaf from Mocchi's singing.

In the forest, Genki is busy with creating battle plans when Wood Golem attacks. No one listens to Genki's battle plans and Genki, Mocchi and Wood Golem falls into the river.

When Genki awakens to find Allan and Mocchi beside him, together with Worms who saved him. It turns out that after Moo's defeat, Allan goes around searching for and unlocking Discs, then he finds them good homes and trainers. Genki is very touched by the change in Allan.

In the Winner's Cup held in a town by the seaside, Mocchi's partner has to be Golem who is the only 1 in the 5 IMA designated monsters that is with the gang. It will be 2 rounds of 1 on 1 battles and a Sudden Death in the event of a tie against the defending champions. While Golem is bend on making up for his mistakes the other time, Mocchi isn't feeling well at all and faints (from high fever) while registering. After being sent to the hospital, they ponder if they should withdraw but Golem decides that he will win the 1st round and even if Mocchi lost, he will win in the Sudden Death round. While on his way to practice, Golem runs into Michelle, a girl who shares much interest in common with Golem. Golem brings her to the beach and she faints from exhaustion.

Pink Jam and the gels who have changed their ways but are still failures in whatever they do. Incidentally, the gang meets up with them (but they don't realize it as they concealed their baddies' crest). Just as things where going well, a fearsome trio of Jokers attacked!

Can Pink Jam do anything about it and can these ex-Baddies be trusted?

The gang meets up with Horn who lost his pirate ship mysteriously one night! Also, they hear about the legend of a phantom ship in these parts of the ocean.

So they decided to help find Horn's ship. Surely, they found the ship alright but it is anything but empty!

When Mum Mew asks about his plans, General Durahan says that he has already found a very strong monster who can deal with the gang.

As they signed up for the World Monster Cup, the gang realized that they don't have a partner for Mocchi that is in IMA's designated list so they went around only to encounter Naga of the Big Bad Four!

Naga says that he has changed and has trained hard to regain his fighting skills and would like to help them out. Everyone but Suezo trusts him.

Naga displays unbelievable fighting abilities but can he be trusted? And what's with this very strong monster General Durahan found?

Mum Mew and Gobi decides to personally deal with the gang and spare the General's monster collection.

The gang enters a training village and splits up to go to their respective type designated region to train. That night, Mocchi gets kidnapped together with other Mocchi Type monsters.

As the plane fly off with the kidnapped monsters, Most appears and rescued some monsters. He then sets off to the kidnappers' base to rescue the others. Mocchi wants to be strong and decides to tag along to learn from the great master - Most.

Will Mocchi return and what is Most's secret?

In General Durahan's collection, there is a fearsome warrior - Shogun who is stronger that General Durahan himself . By accident, Gobi releases this warrior but General Durahan convinced Shogun to defeat the gang who General Durahan says is the strongest around.

Mum Mew and Shogun sets out to find the gang but it appears the Shogun has lost most of his former glory. After Shogun realized that he has been used by the Baddies can he do anything to help Genki and gang?

Tiger meets up with Grey Wolf but refuses to acknowledge him as his brother after realizing that they are opponent in tomorrow's battle! What is Tiger doing?

Tiger isn't his usual self and takes quite a beating from his brother who is very upset about Tiger's behavior. Just then, the Baddies attack!

Just what is going on?

Golem and gang runs into an Old Lady who cooks the best Pizza. Just when she was about to defend her crown in the cooking competition, her secret sauce is stolen!

The ransom is Holly's Mystery Disc! Can they get the sauce back in time to help the old lady defend her crown?

The gang meets up with Granity but then she becomes controlled by a machine type Baddie which enter her head.

Can she fight this control and keep her promise to Big Blue never to do evil again or will she destroy the gang?

Mum Mew, Gobi and Weed tries to capture the gang by issuing wanted posters. When an old hotel owner turns up with the bounty, Mum Mew could neither keep her side of the bargain nor defeat the old hotel owner who is surprisingly well armed!

Mum Mew is forced to find money to pay the old man in exchange for the gang! She tries to rob a bank but finds herself in the middle of a bank robbery by ganstars!

Will Mum Mew finally capture the gang and what will she bring back for General Durahan?

An airplane lifts off from the crash site of General Durahan's ship. Genki and gang made it to the International Monster Association headquarters to register for the Legend Cup. During the conversation with the official, we discovered that Suezo does not know that Mocchi had to fight two monsters to win the Legend Cup. Everyone is surprised and taunts Suezo about it. Suezo felt embarrassed and tried to save his face by saying that he was just trying to make everyone relax.

General Durahan orders Mew and Gobi to show him the highlights of the Legend Cup thus far. Meanwhile, Most's public sparring match is held to raise funds for a gymnasium for young boys and girls as well as monsters that intend to participate in future monster battles.

Despite losing to Most, Most gladly destroys the championship belt to give the Magic Stone to the gang. Armed with the Magic Stone, the gang sets off in Most's plane to find a shrine to unlock the Mystery Disc and seal Moo forever.

However, hot on their trail is General Durahan himself! Can they make it in time?

After rescuing Holly's father, the gang waits for him to awaken. Then, the Mystery Disc gets stolen by General Durahan!

General Durahan, Poison, Weed, Mum Mew and Gobi merge with the Moo to create a powerful armored-clad scarlet warrior.

This new monster appears invincible when all their attacks fail to make an impact on him. Holly's father confronts him and then suddenly a shadow emerges from this monster and engulfs everyone.

Everyone is brought inside the heart of the evil soul and they saw that the evil soul is actually consuming General Durahan, Poison, Weed, Mum Mew and Gobi. Using their powers, they create the Phoenix to fight the evil soul but is that enough?

Will this long and hard struggle finally end?!