Mikey Kudo is a good-natured boy who can't resist helping people in trouble. One day, a strange melody and a mysterious voice reach his ears. Mikey tries to encourage the frail voice that says it's about to be deleted. In front of him, there suddenly appears a Fusion Loader shining with red light. Mikey picks it up without thinking and he's pulled along with Angie and Jeremy into another world.

The Bagra Empire again attacks the Village of Light, where Shoutmon lives. Shoutmon is at a disadvantage, and Mikey helps him combine using Digi-Fusion. Shoutmon asks Mikey to continue fighting alongside him, but Mikey partly for Angie and Jeremy's sakes, says he's going to return to the human world. Shoutmon holds a banquet in a desperate attempt to keep him from leaving. He expresses his fervent desire to become King of the Digital World, and Mikey reacts negatively to this and gets into a fight with him.

Mikey, Angie and Jeremy have become allies with Shoutmon and his fellow Digimon. Meanwhile, MadLeomon's boss, the Bagra Empire Head Officer, Tactimon, unleashes Drimogemon on the Village of Light. Drimogemon causes giant bamboo shoots to grow around the Village, and Jeremy is carried high into the air when he gets caught on one. Christopher, a boy with a blue Fusion Loader, appears and offers to save him if Mikey will join him, but Mikey refuses because he doesn't trust Christopher enough.

What Mikey got his hands on was a Code Crown, proof that one rules a zone in the Digital World. When Mikey and friends follow Nene's instructions and transfer to another zone, they arrive at the Island Zone, which floats in the sea. They ask locals Archelomon and ChibiTortomon where the Code Crown is so they can protect the zone from the Bagra forces who've attacked previously. It turns out it's in a place that can only be reached during the Summer Festival.

Now that he knows the Code Crown is inside Whamon's belly, Neptunemon drops a mixture of giant DigiByte snacks and bombs from the air. Then the island begins to move - because it's actually Whamon, a gigantic Digimon. The plan is to weaken Whamon with the bombing, then find the Code Crown inside his belly, but Shoutmon wards off the bombs with little regard for his own safety. Furthermore, Shoutmon is attacked by Flymon stinger when he and Mikey get inside Whamon's mouth. Whamon rescues the weakened Shoutmon, and entrusts the Code Crown to them when he realizes they want to protect the zone.

Christopher is fighting in another zone and the pretty enigmatic girl Nene arrives to tell him about Mikey's progress. Meanwhile, the island is surrounded by Seadramons and Mikey's team discusses whether to leave behind the captive Archelomon and go to the next zone. The members agree with Mikey that they can't abandon him. Just as Mikey is about to offer the Code Crown and Digi-Memory Card in exchange for Archelomon, Christopher shows up. Mikey refuses Christopher's offer to help them in exchange for the Digi-memory Card and he uses it to summon MarineAngemon. They use their Ocean love attack to distract the enemy and the heroes use a Skyakomon bridge to get to the enemy fleet and rescue Archelomon.