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?!