The Chosen Children cooperate to defeat Apocalymon, with WarGreymon and MetalGarurumon providing the primary attacks while the others provide backup. After taking out Apocalymon's claws and eventually the Digimon itself, Apocalymon refuses to die quietly and decides to take the Chosen and the Digital World along with it with a Suicide Attack. However, the kids refuse to let it end there, and the power of their Digivices contains the attack.
With the Chosen having finally saved the Digital World from its distortions, the kids' Digimon allies congratulate them. The human world goes back to normal and the Digimon vanish from it, while the Chosen's parents look on in happiness. The Digital World reforms itself starting with File Island, and the Digimon who have died are finally able to be reborn at the Village of Beginnings. Takeru, Patamon, Elecmon, and Hikari help the DigiEggs hatch, and the kids and their Digimon allies try to take a picture to commemorate, only for the hatching of a Botamon to spoil the picture.
Ogremon declares that he's going to go traveling and departs, saying that a Virus type like himself shouldn't hang out with Data and Vaccine types. Tentomon expresses distaste at Virus types, but Gennai reminds them that Agumon had become SkullGreymon once and that, while it may have been the wrong evolution for what they needed, there is nothing necessarily wrong with evolution itself.
The kids return to where they spent their first night in the Digital World and relive some nostalgia. However, Jou realizes that because because time flows differently between the human and Digimon worlds, if they leave, they're not sure if theyll ever be alive to see each other again when they return. Yamato suggests staying in the Digital World until vacation is over, which the other Chosen heartily agree to, and Jou calculates that they could spend the Digital World equivalent of 40,320 days (110 years) there. With that, the kids agree to start on their new adventure...
...only to be interrupted by Gennai and Kentarumon, who tell them that a solar eclipse up ahead is the gate that connects the Digimon and human worlds together, and that it will end in two hours, meaning that, if they don't make it, they won't be able to go back. In addition, because Apocalymon is now defeated, the flow of time in the Digital World has now lined up with that of the human world, so they won't be able to spend 110 years in the Digital World, nor will there be any guarantee that the gate will open again anytime soon — and even if they did try to stay anyway, the world might perceive the humans as anomalies and try to erase them. The Chosen Children thus try to spend their last two hours with their Digimon with heartfelt goodbyes.
Sora thanks Piyomon for helping her mend her relationship with her mother, and Piyomon is happy to know that she was more than the bother to Sora she thought herself to be.
Gomamon and Jou tell each other that they had fun being with each other, and Gomamon wishes Jou luck in his exams. Gomamon is finally able to "shake hands" with Jou, finishing off a Running Gag about Gomamon being unable to hold or shake hands with Jou due to theoretically not having any.
While a Mechanorimon makes repairs to the trolley cart, Koushirou apologizes for having imposed on Tentomon so much, and Tentomon remarks on how Koushirou is speaking so formally to him even after all this time. He tells Koushirou not to force himself, and that someday the words will come more naturally to him.
Takeru and Patamon cry together in a field, but Patamon assures Takeru that they'll see each other again, reasoning that they can certainly do so if they were able to reunite after Angemon died fighting Devimon as long as Takeru believes in it. With that, they promise to meet again someday.
Gabumon asks Yamato to play his harmonica for him one more time, and as Taichi hears it, he begins to cry but covers it up and reminisces with Agumon over the time they fought Seadramon. Hikari gives Tailmon her whistle and expresses her goodbye with "until next time", the "next time" of which Tailmon reacts to.
Mimi is unable to find Palmon, and when the kids regroup after their goodbyes at the trolley that will take them home she breaks down crying because she can't say her goodbye to her. Palmon is found by the Gekomon to be crying in the bushes, unable to go see Mimi because it'll hurt too much to say goodbye to her. The Gekomon ask her if that's really what she wants, and if she won't regret it later.
The kids (with a sobbing Mimi) board the train, and Tailmon blows the whistle, starting the trolley on its course towards the gate and back to the human world. The kids wave goodbye to their Digimon, and Mimi hears the footsteps of Palmon outside, who's running after the trolley to apologize and finally say goodbye to Mimi. They wave to each other and Palmon trips over, startling Mimi and causing her hat to fly out of the trolley.
The theme tune "Butterfly" ("Hey Digimon" in the English dub) kicks up as the children wave their goodbyes and the trolley moves farther and farther away from the Digimon, up into the sky. Mimi's hat flies by; the narration tells of how this would not be the last time the Gate opened, and that this would not be the beginning nor the end of the Chosen's adventures and that there would be more adventures as long as they wish for it...
...or at least until the next season.
- Big "WHAT?!": Apocalymon has one when the Digi-Destined reappear before him with their Digimon back at their Ultimate/Mega level forms in the English Dub.
- Taking You with Me: When he's defeated, Apocalymon unleashes his most powerful attack to try to destroy the digital and human worlds and drag them down with him. However, the kids' Digivices activate in response and contain the explosion, preventing it from harming anything.
- This Cannot Be!: In the English dub, Apocalymon states this as he destroyed the Digi-Destined's Tags and Crests, so he believed they could no longer digivolve their Digimon past the Champion level without them.
- Villainous Breakdown: Apocalymon descends into this as soon as he sees the Digi-Destined escaped the Data World and begin gaining the upper hand against him, even when he tries using the same attacks from before and a couple of new ones as well, leading to him being Driven to Suicide with the intent of taking both the Earth and Digital World with him.