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 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 Mocchi manage to climb out of the canyon, and Genki leaves Mocchi (who is caught by a Clay) to free his friends and all of the slaves. The meet Pixie for a showdown, but the ruins collapse while they're fighting, and Big Blue digs them out. Pixie realizes that she is doing what she despises the most by imprisoning the humans, so she decides be join the Searchers' cause.
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.
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?
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...
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.
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.
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.
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.
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! So they had a little sparring session and saw for themselves the immense potential of Mocchi and the younger Wondar, but most important of all, the great friendship between the two. Unknown to the rest, the younger of the brothers actually doesn't like to fight but wants to grow crops all his life but dare not speak up. Later, they part their ways but not before the elder Wondar added some sleeping powder to their stew. His aim is to take their Mystery Disc and hide it so he would not meet them in the next competition! When the Drill Tusks dispatched by General Durahan attacks, the gang finds the disc missing and this led the Drill Tusks to seek and attack the Wondar Brothers! How will it all turn out?!
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. Their opponent is a mild looking boy who acts strangely innocent. Tiger took on a Snail named Knight Nighton but found that his attacks were all useless and lost badly as he could not defend himself. After a tough fight Mocchi defeated his opponent, a much larger Mocchi Type monster and brings the match to Sudden Death! With Mocchi too tired to continue, Tiger volunteers and decides to listen to Genki but will that be enough to win?
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. After some catching up, they decided to help Fairy Hare and get some money for the Orphanage. In town, they rescued Wild Hare (another of Hare's friends) from some Baddies. In the past, the hare trio robs the Baddies and gave to the poor until an unfortunate incident. Acting on Wild Hare's tip and putting their past behind, they decided to rob the Baddies to help others again. Midway, the trio was caught and Holly gave up the Mystery Disc in exchange for their safety. Just as Hare was about to get the Mystery Disc back, Wild Hare stopped him by holding Fairy Hare hostage. This shed some light on that unfortunate incident years ago as Wild Hare has always been working for the Baddies out of jealousy for Hare and Fairy Hare. What will happen to Wild Hare and the Hare trio? More importantly, what's inside Hare's baggage anyway?
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. The professor is touched by Holly and decided to help them but not before they kept their side of the bargain which is to do anything for him (i.e. cleaning, cooking...)! Finally the professor, Genki and Mocchi departed. They found the Mystery Disc in an underwater cave which happens to contain the pirates' treasure! Just then, the Gabus attacked! Can they successfully bring back the Mystery Disc and what will happen to the pirates' treasure?
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. Meanwhile, Golem managed to gain the upper hand against his opponent Cocken (Ducken Type) by using his Tornado attack. However, while Golem was thanking the crowd, Cocken sneaked up and pushed Golem out of the ring and winning the 1st round! In round 2, Mocchi defeated Gabu with Cherry Blossom Blizzard but Suezo still hasn't arrived at the stadium. If Suezo does not arrive, the judges will announce the other team winners by default. Finally the injured Suezo arrives, and found out that he will have to face a gigantic Whale Type monster! Not only is the championship at stake, so is his pride and the kid's cards, can Suezo win?
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. They set off for the second part of the journey and found themselves chased by Durawalls (think: Monol). Sandra's driving and the gang's fighting managed to get them to safety but Sandra still crashed the cab into a forest. Sandra is both injured and upset but Holly managed to cheer her up. With the Durawalls who have a clear advantage chasing them, will they make it out alive?
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. Genki seems to be so confident in his battle plans but not in himself that Allan decides to show him a thing or two with a monster battle between Mocchi and small Worm. Despite Mocchi following Genki's best plans, they still lost to small Worm who surprising managed to make a last minute comeback. Allan tells Genki he cannot win unless he becomes true to himself, like he used to be and leaves. Genki is lost in thought not knowing why he lost, until he saw something Mocchi drew and finally understood the meaning behind Allan's words. The remainder of the gang where still searching for Genki and Mocchi when Wood Golem shows up. Since they don't stand a chance, will Genki arrive in time to save them and does he really have what it takes to win?
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. Golem finds out that she is very sick from her father and that she needs 5000 gold (which is the same amount as the Winner's Cup prize money) for the operation. Golem decides to help, so he trains really hard and asks his friends to let him keep the Winner's Cup prize money. Mocchi looks better after some rest and they enter the competition. Golem managed to defeat a fearsome Arrowhead but Mocchi faints while fighting Noble Gel. In Sudden Death, can Golem defeat the powerful Noble Gel and get the money to help Michelle who came all the way to cheer him on despite her sickness?
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?
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?
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?
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?!