WarGreymon isn't doing so well and is about to be destroyed. Just in time, Whamon jumps out of the water and takes the blast ment for WarGreymon. Whamon destroys MetalSeadramon using his own "River of Power". Whamon is destroyed.  It isn't long after that Puppetmon comes up with an evil plan to destroy the kids. He makes dolls of each of the kids and uses these to make them do what he wants them to. He then separates Matt and T.K. from everyone else. Kiwimon attacks the other kids while Puppetmon corners T.K. T.K. realizes what the dolls are used for and tricks Puppetmon and destroys the dolls. The Digimon easily defeat Kiwimon and Puppetmon says that no matter what it takes he will get revenge on T.K. Matt thinks that T.K. no longer needs him around, so he goes off somewhere by himself.

Just when it looks like it is about over for the kids and their digimon, Whamon shows up to rescue them. Soon after their escape, the Divermon are sent out to look for them. While checking over his computer, Izzy discovers that WarGreymon has the ability to destroy Dramon type Digimon. The Divermon find the kids and attack Whamon, but when Whamon dives down quickly, the Divermon can't follow him because they can't handle the pressure change. Izzy uses his computer to find a tunnel that leads to a safe place...for a while that is. Soon MetalSeadramon finds them and Whamon rushes to the surface and ends up in a bay. When MetalSeadramon attacks, Agumon and WarGreymon WarpDigivolve and prepare for battle.

While trying to save the digidestined from Piedmon, Piximon is destroyed. The kids suddenly find themselves back in the DigiWorld, on the edge of the beach. They soon realize that this is the same spot where they spent their first night in the DigiWorld. Shellmon suddenly attacks them, but the digimon quickly take care of the problem. MetalSeadramon sends Scorpiomon after them. Scorpiomon traps the kids in a building where he almost barbecues the kids. They are only saved when Togemon and Ikkakumon digivolve into mega. The kids then hurry to get away, but get trapped in the middle of the ocean.

The kids and their Digimon find themselves back in the Digiworld. Shortly after coming back, Kari finds Chuumon, a mouse-like digimon, who tells them that a lot of time has passed since they left and now the four Dark Masters have moved the DigiWorld to Spiral Mountain and are planning to take it over. MetalSeadramon shows up but the kids and Digimon are able to escape, they are unable to defeat him because he is an untimate level Digimon. The next Dark Master, Puppetmon, controls the kids and Digimon with strings and drops them off to see the fourth Dark Master, Piedmon. Piximon shows up at the last second and rescues them. The third Dark Master is Unknown at this time.

Agumon and Gabumon warp-digivolve into WarGreymon and MetalGarurumon. Even these two ultimate level digimon can't defeat the more powerful than ever, VenomMyotismon. The digimon combine their attacks and the kids crests begin to glow, destroying VenomMyotismon. Just when the kids think their job is finished, they look up into the sky and see that the digiworld is up above them and up-side-down. They then realize that they must fix things in the DigitalWorld before things in the real world will return to normal. The kids make the hard decision to say goodbye to their parents. A rainbow then appears and pulls them back into the sky which is the Digital World.

Gennai finds a prophecy that could help the kids defeat Myotismon once and for all and restore both worlds. After the kids finally figure out what the prophecy means, they quickly figure out that parts of it are coming true. Bats appear in the sky, the people of Odaiba chant Myotismon's name, and Myotismon returns to his "True" form. Gatomon digivolves into Angewomon. This would make the last part of the Prophecy come true, Angels shoot arrows of light. Angemon and Angewomon shoot arrows at Tai and Matt, this makes Agumon and Gabumon Warp-Digivolve into their ultimate levels.

Kari has just given herself up to Myotismon. Meanwhile, the others are told that in order to defeat Myotismon they must return Kari's tag and crest to her. Gatomon is tricked into telling Myotismon who the eighth child is. Myotismon gets Kari and nearly destroys her, but the other digimon show up just in time to save her. Myotismon makes an attack at Kari and Gatomon, but Wizardmon steps up and takes the full force of the blow and is killed by the blast. Tai gives Kari's digivice to her and Gatomon digivolves into Angewomon. Angewomon strikes Myotismon with her "Celestial Arrow" and it seems that he is gone. However, the kids quickly learn that the battle is not over...The fog has still not lifted.

Tai goes to find his parents and to free the people at the convention center. Izzy receives an email from Gennai telling him how to set up a program on his computer that will stop the evil digimon from finding them. This program ends up saving Tai and his parents. MegaSeadramon attacks Joe and T.K., but Ikkakumon digivolves into Zudomon and defeats the monster. They find Wizardmon in the water with the eighth child's crest. Phantomon shows up and calls two other digimon to attack Sora and Matt. Kari thinks that if she gives herself up to Myotismon, Phantomon will leave them alone, so she gives herself up and Phantomon carries her off.

Myotismon has created a fog that is covering the city of Odaiba, while looking for the eighth child he tells Phantomon to capture everyone in the city. Soon everyone is being held in the Civic Center, including Sora and Mimi. Tai and Matt are caught in the fog, but have not yet been found by the evil digimon. Meanwhile, Joe and T.K. are caught outside the city and are trying to figure out how to get through the fog and back into Odaiba. The people in Odaiba are attacked by DarkTryannomon and Togemon digivolves all the way to the most powerful level, Lillymon, who takes care of the problem. Lillymon goes off to battle Myotismon alone.

Gatomon is watching Kari from the roof of a nearby building, she still isn't sure if Kari is the eighth child or not. Wizardmon finds the eighth digivice in the crows nest. DemiDevimon shows up with Wizardmon and ask what he has found. Wizardmon says that he has found nothing and then takes the digivice to Gatomon. With the digivice, Gatomon suddenly remembers that she has been looking for Kari all of her life. Agumon sees Kari talking to Gatomon and attacks her, not knowing that she and Kari know each other. Agumon's attack is a miss, and Gatomon protects Kari from the blast. Gatomon then reveals to Tai and Kari that she is Kari's digimon and Kari is the eighth digidestined. Myotismon shows up and takes Gatomon away, he knows Gatomon is good and may be able to help him find that eighth child. If he only knew how close he was.

Matt is taking T.K. home on the train, Patamon thinks it was nice that Matt and T.K. where able to spend some time together since their parents are seperated and the two brothers don't live together. T.K. overhears Patamon saying this to the other digimon and thinks Patamon is making fun of them. After that, Patamon leaves the train and Matt and T.K. go to look for him. While looking for Patamon, they run into Pumpkinmon and Gotsumon. Myotismon shows up and when the two refuse to attack the kids, he blasts them back to the DigitalWorld. T.K. thinks it's all his fault that all of this has happened. When Patamon sences that T.K. is upset, he digivolves into Angemon and returns to Matt and T.K. The search for the eighth child now continues…

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.