Tai and the others are looking for the Shibaura area of the city, the search is still on before Myotismon finds the eighth child. Gatomon finds Kari in the park and thinks that she is the eighth child because she did know who Agumon was. Mimi and Sora decide to look for the eighth child in a tower, but once up in the tower, they are attacked by SkullMeramon. Agumon digivolves into Greymon and then to MetalGreymon before he finally is able to beat SkullMeramon.

Tai thinks that Kari may be the eighth child, but he quicklly changes his mind when she doesn't really seem to know much about the digimon.  Tai's cat Miko knocks a digivice out the window. That night, a digimon named Raremon shows up by the beach. While on his computer, Izzy gets an email from Gennai who tells him that he must go after this Digimon himself since everyone else is asleep. Suddenly, Izzy receives a singal from that eighth digivice. Izzy decides to look for the digivice while Tentomon goes after Raremon. Raremon is soon defeated, but a crow picks up the digivice and takes it back to its nest before Izzy is able to locate it.

The DigiDestined have a series of misadventures trying to get back to their homes in Odaiba. Eventually, they end up getting a ride from Sora's cousin, Duane. Later, Duane accidentally pushes Izzy off a bridge. Gesomon attacks and is defeated by Ikkakumon.

The DigiDestined return to their original camp and then head to Highton View Terrace trying to find the eighth child. There, a battle between Garudamon and Mammothmon helps them all recall how they witnessed a battle four years earlier between a Greymon and a Parrotmon. This leads them to surmise that the eighth child must have also seen the fight.

The group travels to Gennai's home where he unravels some secrets about the Digital World. When the kids return to the castle to open the gate, they battle with Dokugumon. Even though the castle is destroyed in the fight, they still manage to open the gateway.

Gennai again appears and tells the kids that there is an eighth DigiDestioned and that Myotismon is planning to go to the Real World with an army of evil Digimon to find him/her. The kids infiltrate Myotismon's castle in an attempt to stop him from opening a gate that will allow him access to the Real World, but fail when Gatomon animates a series of Devidramon statues.

The two groups reunite. Sora tells them about the meanings of each of their Crests and how DemiDevimon told her that her life was loveless and thus her Crest would never glow. Myotismon appears and easily defeats the Digimon. An injured Biyomon goes to help them and Sora's concern and love causes her Crest to glow. Birdramon digivolves into Garudamon and helps the group escape.

Joe and Tai find Mimi being treated like a princess at a palace. Sora convinces her to sing and awaken ShogunGekomom, but ShogunGekomom attacks the kids. MetalGreymon manages to defeat him and Mimi apologizes for her behavior.

Izzy is trapped in Vademon's pocket dimension and robbed of his curiosity. Tentomon eventually reverts back to Pabumon, but manages to snap Izzy out of his trance. DemiDevimon attempts to buy Izzy's Crest from Vademon and, in the confusion, Izzy recovers his Crest and his curiosity. Kabuterimon then digivolves into MegaKabuterimon and defeats Vademon.

Matt, Gabumon, Joe, and Gomamon are being forced to work at Digitamamon's diner to pay off a meal. DemiDevimon sets off a series of accidents that makes Matt question Joe's friendship. Matt overcomes his feelings when Joe is willing to sacrifice himself to save T.K. Matt's Crest glows and Garurumon digivolves into WereGarurumon and defeats Digitamamon.

Tai and Agumon return to the Digital World to find Tokomon. Tokomon relays what has happened in the time that they have been gone (which is several weeks in DigiWorld time). He reveals that the entire group has separated and that DemiDevimon has tricked T.K. into becoming his "friend." T.K. realizes DemiDevimon's trickery after Agumon exposes him for a fraud. Tokomon digivolves into Patamon and drives DemiDevimon away.

Tai and Koromon meet with Kari in Tokyo. They discover that Digimon are appearing in the Real World and decide they must go back to the Digital World to help their friends. After Koromon digivolves into Agumon to battle an Ogremon, a portal opens back to the Digital World.

Tai manages to rescue Sora. Datamon pulls himself, Etemon, and many of Etemon's minions directly into the Dark Network. When Etemon reappears, having fused with the network, Greymon digivolves into MetalGreymon to fight him. The battle ends up opening a portal that sucks away Etemon and transports both Tai and Agumon back to Tokyo.

The discovery of T.K.'s Crest of Hope reveals a cave engraved with Digi-code. Izzy receives an e-mail from Datamon asking for help from within Etemon's headquarters, which is a large upside down pyramid. Datamon promises them that if they free him, he will show them Sora's Crest. After he is freed, however, he escapes and kidnaps Sora. He intends on making a copy of her so that he can control Biyomon.

The group is attacked by a Kuwagamon and Tai fails to digivolve Agumon. Piximon intervenes and saves them. He then offers the group training at his facility, and leads Agumon and Tai into a cave while the others stay outside. When Matt finds his Crest of Friendship and Izzy finds his Crest of Knowledge, they are spotted and attacked by Tyrannomon. Tai and Agumon reappear just in time to defeat Tyrannomon.

After getting lost in the desert, the group is taken aboard a ship helmed by Kokatorimon. Kokatorimon captures all the boys and their partners. Biyomon and Palmon digivolve and defeat him when his ship crashes into a giant cactus. The top of cactus then opens up to reveal Mimi's Crest of Sincerity.

While traveling in the desert, Joe's Tag reacts, leading the group into a Roman-like coliseum. There, they are trapped by Etemon, and Greymon is forced to fight another Greymon. After Joe finds his Crest of Reliability, the group escapes. Tai attempts to force Greymon to digivolve. Greymon digivolves into SkullGreymon and loses control of himself—attacking the others who are unable to stop him. SkullGreymon eventually reverts back to Koromon and apologizes for his behavior.

The kids arrive in a Koromon village overrun with Pagumon, who trick the kids and kidnap Tokomon. Etemon learns of the arrival of the DigiDestined and confronts them. He uses his Dark Network to prevent the Digimon from digivolving and then traps the group inside a cave where they discover their first Crest, Tai's Crest of Courage.

A mysterious person named Gennai appears as a hologram after a fight with Devimon and urges the group to travel to the continent of Server in order to defeat another enemy. Gennai also tells them about objects called Crests that will allow their Digimon to digivolve even further. They build a raft and leave File Island, but are soon swallowed up by Whamon who is still under the control of a Black Gear. After the gear is removed, Whamon takes the kids to where their Tags—the objects that the Crests are stored in—are hidden.

The entire group reunites and is attacked by Leomon. After Leomon is defeated with the light of the Digivices, he tells the children about the prophecies of the "DigiDestined." The group goes back to Infinity Mountain for the final showdown with Devimon. There, Devimon absorbs many Black Gears and grows in size and power—turning the fight in his favor until Patamon digivolves into Angemon and destroys him. Angemon, having used up so much power, reverts into a Digi-egg.