A large number of crows surrounding a bird-shaped flying object has been witnessed in Tokyo. This group is attacking and freeing birds in pet shops and homes one after the other.
Ruli's friend, Mika, and her pet bird fall victim to their attack. Ruli requests Hiro and Kiyoshiro to join them and hear what took place in Mika's home. Later, Hiro tells Ruli that he believes it is a digimon. They plan to start their investigation the next day.
A shady, bird loving man, who was initially attacked has allied with the crows and the object. He agrees with the idea of freeing all birds and creating a utopia. He directs them to where the caged birds reside.
Kiyoshiro's investigation work finds that their ultimate attack will be the Fujinohana Bird Sanctuary!
As Hiro, Gammamon, Ruli, Angoramon, Kiyoshiro, and Jellymon watch over the Bird Sanctuary, the shady man approaches. When the kids try to stop him, he gets Hiro in a headlock. Ruli's quick thinking takes them into the digital world and away from the man. The digimon responsible is Yatagaramon, an ultimate level digimon that controls darkness!
In the digital world, Yatagaramon fights Gammamon, Angoramon, and Jellymon. He overpowers them with his strength. It takes Gammamon's evolution to Kausgammamon to send Yatagaramon on its way. They say Yatagaramon will lead birds to the Golden City but not all birds were following.
Many birds returned to their owners including Mika's precious pet.