As the gang meet up again they are quickly attacked by Beelzemon. However after Beelzemon kills Leomon, Takato, fueled by rage, forces Guilmon to Digivolve to his Mega Form – but it goes horribly wrong and Takato's D-3 Explodes, transforming Guilmon into the terrifying Megidramon.

Gallantmon faces Beelzemon in a tough one-on-one battle. During the battle, Gallantmon destroys Behemoth and rescues Kazu and Kenta which causes them to realize that Takato has merged with Guilmon. Meanwhile, the Sovereign sends his last Deva Chatsuramon to destroy Lopmon for being a traitor. Chatsuramon goes to kill Suzie and Lopmon, but Terriermon takes the hit, saving them and mortally injuring him. Before Chatsuramon can do more, Gallantmon destroys him, taking out the last Deva, but Beelzemon absorbs his data which makes him stronger. Beelzemon beats down Gallantmon and is about to kill him, but Guardromon and Kazu intervene and buy Gallantmon enough time to recover. Beelzemon's attacks do no damage to him after that and he runs out of ammo. Once that's done, Gallantmon blasts Beelzemon with his Shield of the Just, finally defeating him. Gallantmon goes to kill him, but Jeri stops him as it won't bring Leomon back, and orders Takato to spare Beelzemon’s life. Beelzemon remembers his own Tamers and leaves, regretting his actions while Takato gains a new D3 Digivice.

As a strange tiger ultimate level Digimon attacks the tamers begin to fight it. However, when it's too strong for both Rika and Henry, Takato uses the power of the blue card to Digivolve Growlmon into his Ultimate form: WarGrowlmon after a mental conversation with Growlmon where Growlmon informs him he is a worthy to be a Tamer after he doubts himself. WarGrowlmon easily beats and destroys the tiger, Mihiramon. Also, Kazu, Kenta and Jeri witness the battle and are impressed by Takato.

With the unfortunate help of Dark Digivolution, Guilmon digivolves into Megidramon. Megidramon battles Beelzemon and almost has him killed by consuming the demon, but Makuramon comes to confront Beelzemon on how useless his digivolution was. Beelzemon kills Makuramon and breaks free. He kicks Megidramon at his weak point, the chest, defeating him. Megidramon dedigivolves back to Guilmon. Takato goes through deep sorrow and reaffirms his friendship with his Digimon. After making a wish that he could fight, Takato and Guilmon Biomerge to become Gallantmon.

Grani is fully developed. Calumon tries to help awake Jeri. Meanwhile, Beelzemon, released by the D-Reaper, tries to break open the kernel sphere in which Jeri is with no results. He's joined by Gallantmon who manages to use Grani's Yugooth Blaster to destroy the Agent guarding it. Kazu and Kenta are nearly killed, but are saved by Antylamon. During the battle, the adults learn the truth of the Bio-Merging and are shocked. The shots of the kids inside the Digimon is somehow broadcast on live TV and Ms. Asaji leads Takato's entire class in cheering him on once she sees this. Finally Beelzemon manages to break through to Jeri by using Leomon's Fist of the Beast King attack (its indicated with the help of Leomon's spirit) and Jeri finally wakes up, but grows depressed when she realizes its Beelzemon and not Leomon coming to save her. She eventually tries to reach Beelzemon, but its too late and the Kernel Sphere closes up again and Beelzemon is struck down by the D-Reaper and falls towards the Chaos Mass.

During the fight, Gallantmon fell into the D-Reaper and de-Digivolved. Here he met Jeri, but in actual she was a part of D-Reaper. She changed into a D-Reaper digimon called the Agent. Lopmon requested Suzie to help her digivolve so that she could help her friends she digivolves to Antylamon. Calumon senses Jeri in trouble and enlists Impmon's help to rescue her. Impmon, still feeling guilty about killing Leomon, joins him. Calumon knew that Jeri is inside the Kernel Sphere. The Kernel Sphere was the power core of the D-Reaper.

Rika is being followed by a mysterious icy force, which frightens her. Not wanting to admit it, she refuses help when Renamon offers to protect her. Renamon is dismissed, and feels hurt by what Rika said to her. While Rika is vulnerable without Renamon's protection, IceDevimon then appears and captures the girl, taking her into an alternate dimension, an icy tomb where he has sealed his Digimon victims. The fallen angel Digimon offers Rika to be his tamer, but she refuses. Renamon comes to Rika's rescue and digivolves to Kyubimon but fails to stop him. Guilmon and Terriermon attempt to help Renamon and Rika, but are trapped by IceDevimon's freezing ice powers. Finally, Henry manages to free them, and Guilmon takes over the battle. Using extra speed and wings, Guilmon traps IceDevimon's head in the ceiling and destroys him, absorbing his data. However, the traumatizing fear caused by the fight causes Rika to claim she hates all Digimon, and she and Kyubimon go their separate ways.

Rika is having a hard time with her mother, who makes Rika attend a photo session with her. Meanwhile, Renamon has been acting distant and it turns out that she has been meeting with Vajramon, who apparently survived the Tamers' previous battle with them. When Renamon reveals that she has been using Vajramon only to obtain information, the Deva becomes outraged and the Tamers fight him in a second battle. The Tamers prove no match for him until Kyuubimon digivolves to Taomon and destroys Vajramon.

Gallantmon in his new form seems to be making some headway. Meanwhile, the others are losing. In a last attempt Sakuyamon gives all of her power to Justimon who then inserts it into his blade and cuts the Cable Reaper in two, but it proves to be in vain as it regenerates. However, the Digimon Sovereign suddenly appear and drag the Cable Reaper back to the Digital World where they apparently destroy it. The Juggernaut program is revealed to be in MegaGargomon and he activates it in the wormhole vortex. As the vortex is going at the speed of light, the Juggernaut reverses it causing a minture Big Bang and a reverse time effect in it which will devolve the D-Reaper into a harmless program and send it back to the Digital World. Gallantmon Crimson Mode comes into conflict with the Jeri Agent and he finally destroys her before arriving at the cracked Kernel Sphere. Jeri and Calumon are not there anymore as they escaped and Calumon somehow protects them with a forcefield. Unfortunately, the Red Card's effects wear off and the Megas de-digivolve, but Guilmon flings Takato to Jeri and the two are finally reunited. The Tamers try to figure a way out and are suddenly rescued by Kazu, Kenta, Guardromon, MarineAngemon and Lopmon and escape and the D-Reaper is fully sucked into the wormhole and devolves. The Tamers digimon suddenly change to their in-training forms and are forced to return to the Digital World. Before leaving, Impmon asks for Jeri's forgiveness for killing Leomon and she grants it to his surprise. Epilogue – Takato refinds the portal to the digital world at Guilmon's old hiding shed.

The crew meet Zhuqiaomon the Digimon Sovereign. WarGrowlmon, Rapidmon and Taomon face him but are no match for him and Rapidmon's injuries from Chatsuramon leave him weakened and he is indicated to be slowly deleting throughout the episode as he flickers several times. Lopmon tries to help convince Zhuqiaomon to stop but fails and is nearly destroyed by him but WarGrowlmon protects her. Her cries summon Suzie (who was supposed to be watched by Guardromon but he misunderstood Kazu's orders). Rapidmon is defeated and reverts to a severely weakened Terriermon. Henry's determination causes him and Terriermon to BioMerge to MegaGargomon which heals Terriermon's injuries. MegaGargomon defeats and apparently destroys Zhuqiaomon along with his castle and everyone celebrates outside. Unfortunately, Zhuqiamon is revealed to have survived and comes back for revenge.

Ryo and Cyberdromon Biomerge digivolved to Justimon to help them. While MegaGargomon and Sakuyamon go to rescue Takato and Guilmon, Justimon and Guardromon battle another D-Reaper Agent. In the Chaos mass, Kenta and MarineAngemon rescue Takato from the Jeri Agent and they're taken out of there by MegaGargomon and Sakuyamon. Meanwhile, Calumon and Impmon head off to rescue Jeri but are intercepted by more agents. Impmon digivolves to Beelzemon Blast Mode and easily defeats them and he and Calumon reach the Kernel Sphere where they find Jeri. Beelzemon manages to get Calumon into the Kernel Sphere where he joins Jeri, but Beelzemon is captured by the D-Reaper. At the battle with the Agent, Justimon is no match for it even with Guardromon's help and is nearly killed, but Guardromon saves him (something which Kazu is excited about as Justimon thanks him). MegaGargomon and Sakuyamon rejoin the battle, but even their help isn't enough even though they figure out the Agent's weakness. Justimon is nearly killed again but is saved by the sudden arrival of Antylamon who holds the Agent in place, allowing Justimon to finally destroy it. Later, Lopmon apologizes as she witnessed what happened to Beelzemon and Calumon but couldn't stop it so she came to help them instead. As a reward for her help, Ryo gives Suzie a Modify Card to use herself.

Calumon found Jeri in the kernel of the D-reaper. She opened her eyes but didn't respond to Calumon. Meanwhile Takato tried to convince Mr. Katou (Jeri's father) to stop being angry at her. Yamaki was designing a more complex version of the D-Arc which he called "Grani" after a famous warhorse, which he planned to become a steed for Gallantmon. Jeri had flashbacks of when her mother died and began to mutter, frightening Calumon. When a new Agent arrives, Mr. Katou goes to it and pleads for Jeri's release, but is nearly killed. Justimon and Guardromon manage to destroy it, but another bigger Agent arrives. Grani finally arrives and Gallantmon uses it as his steed and rides it up to the Agent and destroys it.

Calumon is being attacked by a digimon and somehow appears in the real world. Meanwhile, a boy named Takato finds a mysterious blue card. His obsession with the Digimon game leads him to create a digimon, and when he finds a Digivice the Digivice copies his created digimon's data and creates a real digi-egg. He has a strange dream involving a Digimon Tamer (who is Rika), and his digi-egg hatches. He finds his created digimon, Guilmon, and fears getting attacked by him.

Rika and Renamon struggle as they contemplate whether or not they need each other to become powerful. Renamon is attacked by a swarm of hostile Flybeemon, but she defeats her enemies and then considers what Impmon told her about becoming powerful without the aid of a human tamer. Later, she is attacked by Harpymon, and finds herself rendered powerless. Renamon is about to be destroyed, when Rika appears and desperately stabs Harypymon with a tree branch to stop her from harming Renamon, allowing Renamon to escape destruction and digivolve into Kyubimon just in time. Kyubimon easily destroys Harpymon but doesn't absorb her data, as she realizes that Rika's friendship as her tamer is truly what she needs to become powerful. Afterwards, Kyubimon and Rika make amends.

The pig deva keeps ploughing through the city and it has to be evacuated. Takato's parents are very concerned because they can't find him but have to evacuate as well. The tamers find themselves outmatched even at matrix level. Henry suggests that he and Rika try believing in themselves and they use Radiant Faith Activate cards. Rapidmon and Taomon knock the Pig Deva down but before they can finish the job the Juggernaut program starts affecting all of them. Henry's dad decides he's had enough and uses his Tai Chi to take down two guards and reach his son. An encrypted code starts attacking the Juggernaut program and as it does the strange child who the kids keep running into reveals himself to be the Monkey Deva and that Calumon is the key to digivolving. At the same time a shining light finds Impmon in the underground tunnel where he's been sulking and offers Impmon power and knowledge to digivolve. The Monkey Deva throws a ball into the Juggernaut tunnel and destroys the program. The pig deva recovers as do Rapidmon and Taomon. Henry's dad and friends reach Takato and the others and tell them about the monkey deva. Takato decides to not be afraid anymore and shows Rika and Henry that if they fight alongside their partners then they can be even stronger. Takato's determination causes WarGrowlmon to gain more strength and after the others deal with Vikarlamon's attacks, WarGrowlmon destroys him with a point-blank Atomic Blaster. Unfortunately, right after, the Monkey Deva, Makuramon, kidnaps Calumon and declares he is taking him back to the Digital World. Leomon tries to save Calumon but is forced back by some shining needles; Jeri receives a Digivice and heals Leomon who is now her partner. In the wake of Vikarlamon's destruction, the Tamers desperately search for a way to enter the Digital World to save Calumon. Hypnos is also destroyed when Makuramon overloads Juggernaught.

After the De-Digivolution of MegaGargomon the tamers came to know that Zhuqiaomon is still alive and still wants to fight. Zhuqiaomon tries to convince Lopmon to turn to his side. When Lopmon refuses to do so, he attacks the tamers. Taomon protects them until Zhuqiaomon is stopped by another Sovereign, Azulongmon. Zhuqiaomon battles him and Guilmon and Terriermon join in to no effect and are nearly destroyed. Takato jumps out of Taomon's shield to help and Guilmon and Takato Digivolve to Gallantmon to fight. Azulongmon lets the battle go on a bit to make a point of how strong Bio-Merged warriors are but ultimately stops the battle and manages to convince Zhuqaiomon that this fight is useless and they should all fight against the real enemy: D-Reaper.

Sakuyamon was formed when Rika bio-merged with Renamon while they took a leap of faith to save Calumon from the D-Reaper. Rika fell back into Renamon and there was a blinding flash of blue light. The two Bio-Merge into Sakuyamon and drive back the chaos, rescuing Calumon, but the D-Reaper quickly recovers.

Takato, Rika and Henry reunited to fight against the D-Reaper but they failed to defeat it as they realized that they can not Biomerge to Mega form in this world as they are not data in this world. Impmon meets his friends Ai and Mako. They treated him nicely. When Impmon saw the Tamers on TV fighting the D-Reaper, he decides to help them even though he's not sure he can Digivolve again. Ai gives him a kiss and Mako gives him a toy gun and he heads off to help. Impmon's determination to help causes him to digivolve to Beelzemon again, and Mako's toy gun causes him to digivolve further into Beelzemon Blast Mode with the toy gun as his new weapon. Beelzemon turns the tide of the battle, weakening the D-Reaper's Agent allowing WarGrowlmon, Rapidmon and Taomon to destroy it. Afterwards the Tamers and their Digimon joke around with Beelzemon who is at first annoyed, but joins in when he figures out they're just joking around. Takato sees Jeri mysteriously nearby.

The Tamers enter the D-Reaper to fight and to rescue Jeri. At Hypnos, everybody is working on Operation Doodlebug that is supposed to revert the D-Reaper to its original harmless form using the Juggernaut program. The D-Reaper opens a wormhole connecting it to the D-Reaper in the Digital World and summons the Cable Reaper. Sakuyamon destroys some of the Agents which frees Jeri. Jeri's own determination boosted by Calumon causes her to start to fight again and the Kernel Sphere is cracked by her Digivice although Chaos Mass starts to flow in. Outside, some cops are attacked by an Agent but they're rescued by Kazu, Kenta, Guardromon and MarineAngemon who are then surrounded by police (it is never explained how they get away). Impmon, Ai and Mako escape the city on a bus, but Impmon is seriously injured and doesn't know if he'll survive. Suddenly a Dig-Nome grants Ai and Mako a Digivice which heals Impmon and officially confirms the two as his tamers. Gallantmon tries to reach the top of the Mother D-Reaper but falls. Grani then approaches him asking if he wants wings to fly. Grani sacrifices itself and enables Gallantmon to become Gallantmon Crimson Mode.

Impmon is scaring couples at night in the park, but Takato suspects Guilmon of causing this trouble. Impmon takes Guilmon out and when Takato finds him missing he suspects more of him. When Guilmon comes back, not knowing what's happening, he says he scared a couple and Takato gets really mad at him. Later, Devidramon appears and fights Guilmon and Renamon refuses to join as its Guilmon's fight, not hers. Takato forgives Guilmon after finding out about Impmon, and Guilmon digivolves to Growlmon and destroys Devidramon.

Impmon is defeated by Indramon; Indramon then seems to self destruct willingly. Mr. Wong is introduced to the Juggernaut program and is asked to help destroy the Digimon. Indramon rematerializes, and the Tamers commence battle. The Tamers prove no match for Indramon and he isn't even scratched by theirs or the military's attacks. In a desperate move, Takato tries the Blue Card his friend Kazu made for him and Growlmon digivolves to WarGrowlmon again. WarGrowlmon easily destroys Indramon leaving Kazu very pleased with himself.

A string of earthquakes are disturbing the city. The friends meet at Guilmon's hideout and while Rika helps Jeri learn about digicards Henry shows everyone that the devas are patterned after the Chinese horoscope animals. A weird boy who has been secretly watching Calumon comes into the open and the kids run after him. When the Pig Deva – Vikarylamon appears Yamaki freaks out again and initiates the Juggernaut program despite Henry's dad protesting that it will hurt the children's good digimon. The partners track the Pig Deva down but even after digivolving to Growlmon, Gargomon, and Kyubimon they are unable to affect the deva at all. Wishing for help, the tamers find that if they wish to protect others they can matrix digivolve.

The group returns to the desert to try to find Rika. Rika nearly drowns but is unexpectedly saved by Calumon. A flood pushes them and Renamon to the desert and Calumon digivolves Renamon to Kyubimon to save them. They reunite with the others, but before they can return home, they get confronted by Beelzemon who Kyuubimon realizes is the Digivolved Impmon. Kyubimon digivolves to Taomon to face him, but unfortunately the Dog Deva, Chatsuramon, shows up and recaptures Calumon. Unfortunately, while Yamaki is on leave, the government starts up the Juggernaut, causing sudden night and storms in the Digital World. Thanks to Chatsuramon's attack, Henry, Takato and Terriermon get sucked into a data stream while the others are protected by a shield from Taomon and Beelzemon runs off. At Hypnos as the Juggernaut gets out of control, one of the agents calls Yamaki and Riley and they manage to shut it down.

Calumon helps every digimon in the digital world to Digivolve to Mega so that they could fight their real enemy the D-Reaper. Meanwhile, Kenta meets a MarineAngemon who grows attached to him, but he sends to battle. Azulongmon sends the Tamers to the desert world to return home and while Zhuqiamon is still disgusted by the Tamers Digimons choice, he decides to respect that and allow them to go with the Tamers.

A mysterious girl arrives with a Digimon Dobermon. They were sent by Azulongmon to make the Tamers able to Biomerge to Mega level. They came to know that Dobermon is a gift and he sacrifices him to make them Biomerge digivolve. They were told that the major part of D-Reaper is in the real world and it's up to them to stop this.