Genki is a boy who loves playing the Monster Rancher games and one day he's somehow transported into the world of the video game where he meets the girl Holly and the monsters Mochi, Suezo, Golem, Tiger and Hare. Together, they are searching for a way to revive the Phoenix, which is the only monster capable of stopping the evil Moo.
Episode 1
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?
Episode 2
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.
Episode 3
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!
Episode 4
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.
Episode 5
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.
Episode 6
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.
Episode 7
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!
Episode 8
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.
Episode 9
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.
Episode 10
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?
Episode 11
After scaling a cliff, Genki and Mocchi must free their captured comrades and find a way to defeat Clay, Pixie, and Big Blue!
Episode 12
In search of a mysterious disk, Monol tells of a great story from the past.
Episode 13
Genki and friends meet paths with the infamous Moo. Will they be strong enough to defeat him?
Episode 14
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.
Episode 15
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.
Episode 16
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!
Episode 17
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?
Episode 18
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.
Episode 19
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?
Episode 20
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.
Episode 21
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.
Episode 22
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.
Episode 23
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?
Episode 24
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.
Episode 25
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?
Episode 26
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.
