Floating on the bed, Joe and Gomamon are at sea. They are attacked by Ogremon, but Gomamon digivolves to Ikkakumon and defeats him. After the fight, the two are rescued from drowning by Sora and Biyomon, who pull them back to shore with a fishing rod. They come upon a church service. The people at the church are ghosts called Bakemon. Gomamon and Biyomon digivolve to Ikkakumon and Birdramon to fight the Bakemon, and with the help of some quick thinking by Joe, they defeat him. With the enemy defeated, the two kids and their Digimon go off to find their friends.
T.K. and Patamon, still separated from the others, arrive at Primary Village, which is full of bright colors, fun shapes and lots of Baby Digimon. Elecmon, caretaker of the Baby Digimon and Digieggs, shows up and fights with Patamon. When the babies start crying, though, T.K. convinces the Digimon to settle their differences in a tug of war, which Patamon wins. As a result of the duel, T.K., Patamon and Elecmon learn the value of joining together and sense that when their hearts are as one, the shattered File Island will return to normal. Devimon, of course, has other plans for the kids and the Digital World…
T.K. and Patamon are attacked by Leomon and Ogremon. The rest of the kids arrive and use their Digivices-devices that destroy Black Gears-on Leomon, returning him to his good self. Leomon tells the kids of the legend of the "DigiDestined," who will bring peace to the island. The kids realize they might be able to return home if they destroy Devimon, so they go after him. When it becomes clear that the Digimon aren't powerful enough to defeat Devimon, even in their digivolved states, Patamon digivolves to Angemon. He uses all his power to destroy Devimon and devolves into a Digiegg.
Gennai asks the kids to come to the continent of Server to defeat his enemies. He tells them that if they can find certain tags and crests that Devimon hid, their Digimon will be able to digivolve to the next level. The kids and their Digimon sail a raft to Server, but they're swallowed by Whamon en route. They remove a Black Gear from Whamon's stomach, and in return he takes them to where Devimon hid the tags. The kids and their Digimon defeat Drimogemon, remove his Black Gear, and recover the tags.
The kids arrive at Server and encounter a village inhabited by Pagumon, tricksters who, with the help of the Gazimon, have imprisoned the real inhabitants of the village, the Koromon. The kids rescue the Koromon and the Pagumon leave, but Etemon and his Dark Network appear and destroy the village. When the Digimon try to digivolve to fight him, Etemon stops them with his rock 'n' roll Concert Crush. The kids and their Digimon are forced to flee into a cave, where Tai finds the Crest of Courage.
Izzy explains that to digivolve, the Digimon need two things: their human partner must be in danger, and they must have a lot of energy. Since he's the only kid with a crest, Tai stuffs Agumon with food so he'll have the energy to digivolve to his ultimate form if it's needed. Joe's tag leads the group to a Coliseum where his crest should be, but Etemon sends an evil Greymon to attack them. Agumon digivolves to a new form, SkullGreymon, a savage killing machine. SkullGreymon defeats evil Greymon, then turns on the other Digimon before he runs out of energy and digivolves back to Koromon. Joe finds his crest.
The kids and their Digimon are walking through a barren desert when Gennai appears to tell them that they must take care of their Digimon or they won't digivolve properly. Suddenly, a huge cruise ship appears. Everyone boards it, but it turns out it's piloted by Cockatrimon, one of Etemon's henchmen. He captures the boys and turns their Digimon to stone, then corners the girls. Birdramon and Togemon fight him off, freeing the boys and their Digimon, and everyone flees, but Cockatrimon chases them in his ship. Then a giant cactus appears and destroys the ship. Mimi finds her crest, the Crest of Sincerity.
The kids and their Digimon are still walking through the desert in search of crests when they're attacked by Kuwagamon. Agumon, troubled by his experience as SkullGreymon, is afraid to digivolve, and things look bad until Piximon, a famous trainer of Digimon, appears and saves them. Piximon takes them to his home and trains the Digimon. Tyranomon, one of Etemon's henchmen, attacks, and the value of Piximon's training is proven when Agumon digivolves to Greymon and defeats the ferocious monster. Matt and Izzy find their crests.
Answering an e-mail plea for help, the kids learn the secret of the DigiWorld-it's actually a computer program, and everything in it (including the kids) are just data given form. This knowledge makes Tai feel invulnerable-his real body is safe in the real world. The kids find the source of the e-mail, Datamon, a robot who's been held prisoner by Etemon for years. The kids free Datamon, but he turns on them and kidnaps Sora and Biyomon before fleeing. Tai starts to go after them, but he hesitates when Izzy warns him that any damage he takes in the DigiWorld will affect his real body. Datamon escapes with Sora and Biyomon.
The kids go after Datamon, who has kidnapped Sora and Biyomon. While the others provide a diversion, Tai and Agumon enter his pyramid, where he's trying to make a copy of Sora. Tai and Sora are able to get away when Etemon and his forces burst in to attack Datamon. Datamon tries to drop Etemon into a black pit, but he, the pyramid, and Etemon's forces are dragged in, too. Etemon manages to escape and prepares to attack the kids. Fortunately, Greymon successfully digivolves to his ultimate form, Metalgreymon, and is powerful enough to defeat Etemon. But as he does so, he and Tai are dragged into the black pit-a dimensional rift.