Takuya Kanbara, Koji Minamoto, J.P. Shibayama, Zoe Orimoto, Tommy Himi, Bokomon, & Neemon ride a Trailmon (Ball) through a desert when they get caught in a battle between human and beast Digimon. It is interrupted by the Lost Island, an island trapped between dimensions, crashing down between them and scooping all involved up.
Takuya, J.P., and Tommy end up in the human-controlled village with Kotemon, just as tanks come in. At Takuya's questioning, Kotemon explains that the island is protected by their guardian god Ornismon, and Bokomon points out when a mural of Ornismon as well as AncientGreymon, and AncientGarurumon of the Ten Legendary Warriors. Their conversation is interrupted by attacks from the beast Digimon, who commit a suicide attack when faced by Dinohyumon. Dinohyumon confronts Hippogriffomon, the leader of the beast Digimon, who escapes. Dinohyumon and his troops give chase, only for Darcmon, the leader of the human Digimon, to attempt stop him in favor of peace.
Meanwhile, Zoe and Koji end up in a beast-controlled town, tended to by Bearmon. Suddenly, human Digimon, led by Dinohyumon, attack, and Grizzlymon confronts them. The attackers are repelled, and Dinohyumon flees as Hippogriffomon appears and advocates attacking.
Kotemon then leads Takuya's group to Koji's group in a neutral meeting location, where the two sides argue over who is at fault, only for Bearmon, Kotemon, and various Fresh Digimon to stop them by crying. The DigiDestined stop their bickering in the face of the combined forces of the children's tears and their friendship. The Digimon lead them to an ancient mural of Ornismon, which has ancient DigiCode written on it that Bokomon begins to translate though the text is fragmented and incomplete. Their peaceful meeting is broken up Dinohyumon and Grizzlymon fighting, and the children's tears are ignored by the elder generation. In anger, Takuya and Koji spirit evolve to Agunimon and KendoGarurumon to stop them. Dinohyumon and Grizzlymon end up separating the two friends, leaving a solemn atmosphere behind.
Right before a major battle, Darcmon issues a speech to stir up the crowd for a final battle. Dinohyumon tries to recruit Takuya because he spirit evolved into the human-type Agunimon, and he agrees as a distraction to allow Tommy to escape with Kotemon. J.P. escapes as well. Hippogriffomon provides a similar speech for the beast Digimon, and Grizzlymon makes an identical offer to Koji for similar reasons. Koji also agrees, as it allows Zoe and J.P. to escape with Bearmon. As the opposing forces gather, Zoe, J.P., Tommy, Bearmon, Kotemon, Bokomon, Neemon, and many Fresh Digimon gather at the mural and attempt to piece together the writing beneath it. They manage to finish, but the battle begins, and the effects force them to restart.
As the Digimon slaughter each other, Takuya and Koji cannot take it any longer. They spirit evolve to BurningGreymon and Lobomon and attempt to stop the fight without killing anyone. This draws the ire of both forces and makes them targets. Meanwhile, the other group finishes the mural, where Bokomon discovers the Ornismon is no protector but rather an evil being that oppressed the island, and that the battle is to revive him through hatred. They discover a ornament missing with the same shape as items carried by both Darcmon and Hippogriffomon. Zoe and J.P. head out to inform Takuya and Koji what they learned, while Tommy and the others stay to finish the mural of AncientGreymon and AncientGarurumon in hopes that they can find an answer to the crisis.
The battle rages, and Zoe and J.P. discover a horrible secret: Darcmon and Hippogriffomon are the same Digimon, as they see Darcmon turn into Hippogriffomon right before them. They spirit evolve to Kazemon and Beetlemon to catch everyone's attention, but they are too late. Darcmon collects all of the Fractal Code and revives Ornismon, while Tommy spirit evolves to Kumamon to protect the kids. Darcmon then assumes his true form of Murmukusmon and mounts Ornismon as the DigiDestined rally to fight him. They are unable to harm the pair, and Murmukusmon guides Ornismon to the murals of AncientGreymon and AncientGarurumon, which begin shining. Kotemon gives his life to protect them, and Bearmon's tears along with Kotemon's sacrifice summons spectral forms of the dead Warriors. Their appearance gives the DigiDestined a second wind, and this time the other Digimon aid in the fighting. In the confusion, Agunimon takes out Murmukusmon, and the Legendary Warriors defeat Ornismon, returning peace to the land.
The Lost Island returns to the Digital World, now with the warring Digimon at peace and committed to rebuilding. At the very end, Kotemon turns up alive, and he and Bearmon have a tearful reunion.
- Junko Takeuchi as Takuya Kanbara, Agunimon & BurningGreymon
- Hiroshi Kamiya as Koji Minamoto, Lobomon & KendoGarurumon
- Sawa Ishige as Zoe Orimoto & Kazemon
- Michael Shitanda as J.P. Shibayama & Beetlemon
- Kumiko Watanabe as Tommy Himi & Kumamon
- Kazuko Sugiyama as Bokomon
- Masami Kikuchi as Neamon
- Taeko Kawata as Kotemon
- Akemi Okamura as Bearmon
- Yuji Ueda as Dinohumon
- Kenta Miyake as Grizzlymon
- Hikaru Midorikawa as Hippogriffomon
- Ken Yamaguchi as Murmukusmon
- Takako Uehara as Darcmon
- Dave Wittenberg as Takuya, Agunimon & BurningGreymon
- Steve Staley as Koji, Lobomon & KendoGarurumon
- Michelle Ruff as Zoey & Kazemon
- Steve Blum as J.P. & Beetlemon
- Brianne Siddall as Tommy & Kumamon
- Brian Beacock as Bokomon
- Michael Sorich as Neamon
- Debi Mae West as Kotemon
- Wendee Lee as Bearmon
- Doug Erholtz as Dinohumon
- Peter Spellos as Grizzlymon
- Wally Wingert as Hippogriffomon
- Bob Papenbrook as Murmukusmon
- Tara Platt as Darcmon
- The English version uses the original name of "DigiCode" for what is termed "Fractal Code" in the series.
- Some scenes cut from the movie include several Beast Digimon getting smashed into walls by several Human Digimon.
- Any of Kazemon's attacks that involved close-up shots of her buttocks are briefly cut out.
- The DigiDestined are divided into two groups when they land on the island; Takuya, J.P., and Tommy on the Human side, and Koji and Zoe on the Beast side. This matches how their respective Spirits were originally divided between Seraphimon and Ophanimon.
- While the three previous Digimon movies use the American Frontier opening theme, this movie does not.
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