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.

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.