Shoutmon holds a banquet in a desperate attempt to keep Mikey from leaving the Digital World. The evil Bagra Army attacks and Shoutmon is at a disadvantage, until Mikey helps him combine with his Digi-friends using Digi-Fusion.
Mikey, Angie and Jeremy have become allies with Shoutmon and his fellow Digimon. Still trying to defeat the Bagra Empire, they meet Christopher and Nene, two other humans living in the digital world. Will Christopher and Nene help Mikey? Or do they have plans of their own?
With proof that controlling a Code Crown makes you the ruler of that zone, Mikey and Team Fusion Heart go in search for the Island Zone's Code Crown in order to protect it from the Bagra Forces.
Evil Neptunemon learns the Code Crown is inside Whamon's belly, so he drops a mixture of DigiByte snacks and bombs from the air to weaken the gigantic Digimon. But Shoutmon wards off the bombs with no regard for his own safety.
Local Digimon have been rounded up by AncientVolcanomon in an attempt to excavate the Code Crown at the ruins where the Bagra base is located. Just as Mikey's team tries to rescue the Digimon from prison, the enemy discovers them.
Mikey and Team Fusion Heart allow themselves to be captured by AncientVolcanomon so they can learn where the Digimon prisons are located. Meanwhile, Bagra Empire Head Officer Tactimon reveals that Dorulumon has acted as his right hand in overthrowing numerous zones in the past.
While Mikey and Dorulumon await their fate in a cell, Christopher shows up to fight Tactimon just in time. When a past friend of Dorulumon remembers he owes him one, he lets them run free.
Mikey goes to the Lake Zone and saves Knightmon from the bottom of an icy lake. Meanwhile, the Bagra forces led by IceDevimon attack the castle under orders from Laylamon. Christopher and crew arrive and fight alongside Mikey.
Since Mikey is too exhausted to battle, the Fusion Fighters band together under Jeremy's leadership. Angie becomes concerned when she hears Beastmon talking in her sleep about how both the Digital World and the human world are facing a crisis.
While looking for treasure in the Sand Zone, Team Fusion Heart ends up falling into an underground Bagra Base. Pharoahmon and Deputymon test Mikey's team to see if they are worthy of the Code Crown.
When Reapmon observes the goddess statue emit light to Mikey, he recalls his past with the Warriors of the Goddess who were tragically destroyed. Meanwhile, Laylamon brings along Ebemon and attacks the Fusion Fighters.
Mikey and the Fusion Fighters are surrounded by the enemy while Reapmon takes part in a healing ritual. When Reapmon sacrifices his own self for the rest of the team, he is reborn as Beelzemon.
Mikey and friends are forced to the Sky Zone where the police presence is so strong the Bagra Empire can't touch it. Visiting the Art Gallery, the Fusion Fighters and their new friend, Lucemon are charged with crimes they didn't commit and ultimately arrested and taken to the deletion site!
Lucemon wins the support of the zone's Digimon and becomes the new president. After his election he reveals his hidden wicked nature. ShoutmonX4B gets the better of him as he tries to deliver the Code Crown to Laylamon.
Mikey asks Sparrowmon to work with him to save Nene. Sparrowmon then tries to get DarkKnightmon to help them, but DarkKnightmon is more interested in increasing the power of darkness in Lucemon's vicinity.
Mickey and Shoutmon are separated from Angie and Jeremy as they enter the Jungle Zone. As Jeremy and Angie hide in a temple, Dorulumon returns to Mikey while Tactimon leads Bagra forces to close in on Mikey and Shoutmon.
The Fusion Fighters follow AxeKnightmon and Nene into the jungle's sacred zone in search of the mighty Digimon Deckerdramon. Mikey finds out that Nene is under AxeKnightmon's control for the sake of her younger brother. Now Mikey needs to find a way to help Nene!
Mikey reunites with the Fusion Fighters in the Dust Zone after getting abducted and released by AxeKnightmon. But ToyAgumon's gang shows up and steals the Fusion Loader. Shoutmon and crew have a hard time fighting back against GrandLocomon's merciless attack, but they combine forces with the local Digimon and manage to take back the Fusion Loader.
Mikey's team goes to rescue Nene from prison, but a mind-controlled Christopher stands in their way. Meanwhile, the team is still in search for the Code Crown.
Mikey's stuck between zones, until he's picked up by Wisemon, a researcher who wants to learn everything about the Digital World. Mikey learns that the digital world existed since the ancient past and the human section is just a small portion. Meanwhile, Arukadhimon catches the Fusion Fighters.
Mikey's team comes to the Shinobi Zone, where it's under attack by Bagra forces led by Musyamon, who has captured the Monitamons' castle and princess. There they learn from Monitamon elder that in order to get the Code Crown, they'll have to make its owner, Karatenmon, laugh.
Mikey's team defends the Monitamon village and works to rescue the Princess. When Musyamon has Jeremy in a tight spot, the unconfident Monitamons and Nene come to help him. Seeing how the members care for each other, Nene again tells Mikey that she wants to be part of the Fusion Fighters.
When Mikey's team comes to the Disc Zone, they discover Christopher is fighting Blastmon in an effort to hang on to the Code Crown. Mikey tries to help him in order to keep the fighting from collapsing the zone, but the ground caves in and the main attackers from both teams fall to the zone's lowest level.
When Mikey is able to return the Fusion Fighters and the residents of the Disc Zone to the Shinobi Zone, Shoutmon questions his ability to keep being the core of all these Digi-Fusions.
Team Fusion Heart works together in a bake-off against WaruMonzaemon to rescue the chefs of the Sweet Zone. Cutemon learns from the rescued pastry chef Digimon that his parents were among the captive Digimon.
Mikey's team slips and falls into the town's underground, where they are attacked by Raremons, but manage to escape and search for the town's captive Digimon and Cutemon's parents.
Mikey, Jeremy, Angie and Shoutmon are back home. Meanwhile, Tactimon has ended up in the human world too, and he revives himself by absorbing digital energy. Now Mikey, Jeremy and Angie must decide if they should head back to the Digital world.
