"Mikey Goes to Another World!" ("Taiki, Go to Another World!") Transcription: "Taiki, Isekai e Yuku!" (Japanese: タイキ、異世界へ行く！)

"He is Shoutmon, Hear Him Roar!" ("Shoutmon, Roar!") Transcription: "Shautomon, Hoeru!" (Japanese: シャウ卜モン、吠える！)

"A Rival Appears" ("Rival Kiriha, Appear!") Transcription: "Raibaru Kiriha, Arawaru!" (Japanese: 強敵キリハ、現る！)

"Island Zone in Chaos!" ("Island Zone, Upheaval!") Transcription: "Airando Zōn, Gekidō!" (Japanese: アイランドゾーン、激動！)

"Thanks for the DigiCards!" ("Digimemory, Shine!") Transcription: "Dejimemori, Kagayaku!" (Japanese: デジメモリ、輝く！)

"Crisis or Conquest" ("X4, Crisis Breakthrough!") Transcription: "Kurosu Fō, Kiki Toppa!" (Japanese: ×4, 危機突破！)

"Danger Erupts!" ("Volcano Digimon, Explosion!") Transcription: "Kazan Dejimon, Daibakuhatsu!" (Japanese: 火山デジモン、大爆発！)

"Meltdown in the Magma Zone!" ("Fierce General Tactimon, Close In!") Transcription: "Mōshō Takutimon, Semaru!" (Japanese: 猛将タクティモン、迫る！)

"Dorulumon's True Colors!" ("Dorulumon, Run Like the Wind!") Transcription: "Dorurumon, Kaze ni Kakeru!" (Japanese: ドルルモン、風に駆ける！)

"The Rival Champions!" ("Taiki, Become a Knight!") Transcription: "Taiki, Kishi ni Naru!" (Japanese: タイキ、騎士になる！)

"Ice to See You, Angie!" ("Xros Heart, Burn!") Transcription: "Kurosu Hāto, Moeru!" (Japanese: クロスハート、燃える！)

"Treasure, Traps and Trouble - Oh My!" ("Sand Zone, A Great Adventure in the Ruins!") Transcription: "Sando Zōn, Iseki de Daibōuken!" (Japanese: サンドゾーン、遺跡で大冒険！)

"Mikey, Warrior of the Light!" ("Taiki, Warrior of the Goddess!") Transcription: "Taiki, Megami no Senshi!" (Japanese: タイキ、女神の戦士！)

"Showdown in the Sand Zone" ("The Warrior Beelzebumon, Dances!") Transcription: "Senshi Beruzebumon, Mau!" (Japanese: 戦士ベルゼブモン、舞う！)

"Trouble in Paradise" ("Heaven Zone, The Trap of Paradise!") Transcription: "Hebun Zōn, Rakuen no Wana!" (Japanese: ヘブンゾーン、楽園の罠！)

"A Dark Cloud Over the Sky Zone" ("The Dark Knight Digimon Arrives!") Transcription: "Kurokishi Dejimon, Sanjō!" (Japanese: 黒騎士デジモン、参上！)

"Clash in the Clouds" ("The Miraculous DigiXros! Shoutmon X5 Flies!") Transcription: "Kiseki no Dejikurosu! Shautomon Kurosu Faibu Tobu!" (Japanese: 奇跡のデジクロス！シャウトモン×5飛ぶ！)

"Welcome to the Jungle Zone!" ("Stingmon, the Great Digimon Forest's Hero") Transcription: "Sutingumon, Dejimon Dai Mitsurin no Yūsha" (Japanese: スティングモン、デジモン大密林の勇者)

"Rumble in the Jungle Zone!" ("The Legendary Deckerdramon, Moves!") Transcription: "Densetsu no Dekkādoramon, Ugoku!" (Japanese: 伝説のデッカードラモン、動く！)

"Train of Terror!" ("Dust Zone, Grand Locomon's Big Scrap City!") Transcription: "Dasuto Zōn, Gurandorocomon no Dai Sukurappu Toshi!" (Japanese: ダストゾーン、グランドロコモンの大スクラップ都市！)

"Disaster in the Dust Zone!" ("Decisive Battle! DarkKnightmon VS Xros Heart!") Transcription: "Kessen! Dākunaitomon VS Kurosu Hāto!" (Japanese: 決戦！ダークナイトモンVSクロスハート！)

"Lost in Digital Space" ("Wisemon, the Secrets of the Digital World!") Transcription: "Waizumon, Dejitaru Wārudo no Himitsu!" (Japanese: ワイズモン、デジタルワールドの秘密！)

"Laughing All the Way to the Code Crown" ("Shinobi Zone, The Comical Ninja Battle!") Transcription: "Shinobi Zōn, Owarai Ninja Batoru!" (Japanese: シノビゾーン、お笑い忍者バトル！)

"Monitamission Impossible!" ("Dropout Monitamons, Do Your Best!) Transcription: "Ochikobore Monitamonzu, Ganbaru!" (Japanese: 落ちこぼれモニタモンズ、がんばる！)

"Showdown in Shaky Town!" ("Zone Collapses! Sparks Fly Between Taiki and Kiriha!") Transcription: "Zōn Hōkai! Hibana Chiru Taiki to Kiriha!" (Japanese: ゾーン崩壊！火花散るタイキとキリハ！)

"Shoutmon - Bogus King or the Real Thing?" ("Shoutmon, Proof of a King!") Transcription: "Shautomon, Kingu no Akashi!" (Japanese: シャウトモン、キングの証！)

"Sweet Zone Bake-Off!" ("Sweets Zone, Sweet Tooth Digimon Battle") Transcription: "Suītsu Zōn, Amatō Dejimon Batoru" (Japanese: スイーツゾーン, 甘党デジモンバトル)

"Battle in the Digital Depths" ("The Ultimate Weapon Active! Hang in there Cutemon!") Transcription: "Saishū Heiki Hatsudō! Ganbare Kyūtomon!" (Japanese: 最終兵器発動！がんばれキュートモン！)

"Fall of the Final Code Crown" ("Taiki & Kiriha VS the Bagra Army, a Complete Showdown!") Transcription: "Taiki Kiriha VS Bagura Gun, Zenmen Kessen!" (Japanese: タイキ・キリハVSバグラ軍、全面決戦！)

"When Worlds Collide" ("Brand New Journey!! Tokyo Showdown!!") Transcription: "Arata Naru Tabidachi!! Tōkyō Daikessen!" (Japanese: 新たなる旅立ち！！東京大決戦！！)

Mikey Kudo and Shoutmon return to the Digital World and land in what they learn to be known as Dragonland from Shoutmon's old friend named Lilymon. Lilymon reveals that the Digital World has been formatted by Lord Bagra into seven lands with the Bagra Army's Dark Fortress in the center. The three see a faction of the Bagra Army under the command of Dorbickmon who is known as the Fire Fury. Dorbickmon is one of the seven Dark Generals overseeing the lands.

With OmniShoutmon trapped, Dorbickmon assumes his Darkness Mode One form to force the Digimon back to his rookie form. Mikey Kudo, OmniShoutmon, and Christopher Aonuma are saved by who they later learn is Nene Amano. Nene used special pollen that weakens dragon type Digimon.

With Dorbickmon defeated, Mikey Kudo, Christopher Aonuma, and Nene Amano open the gate to the next land with Wisemon confirming that negative energy is also passing through the gate portal towards the Code Crown. Christopher takes another route. The Fusion Fighters arrive at another land where they managed to help a Lopmon escape from a red LadyDevimon and her two LadyDevimon aides when unable to destroy them.

As Mikey Kudo, Christopher Aonuma, and Nene Amano find themselves in a pinch, NeoMyotismon reveals that he had made himself immortal by absorbing all the Lopmon that his forces brought to him after absorbing MetalGreymon to assume Darkness Mode Two form. NeoMyotismon was about to absorb Shoutmon ×5 when he is spooked by Lopmon making himself glow white.

After destroying NeoMyotismon, Mikey Kudo, Christopher Aonuma, and Nene Amano arrive to Honey Land where they encounter a group of Digimon that had their energy drained. The Fusion Fighters discover that Lilamon is under attack by a swarm of Honeybeemon who drain her energy. The Fusion Fighters try to save her, but they are stopped in their tracks by a Digimon named Ignitemon. Ignitemon weakens the Fusion Fighters’ Digimon under orders from the miniature Dark General named ...

After Zamielmon escaped during their fight against GrandisKuwagamon, Mikey Kudo, Christopher Aonuma, and Nene Amano discuss how to defeat such a small opponent. However, Ignitemon reveals that Zamielmon eats DigiHoney to shrink with Mikey having a plan to fight the Dark General at his true size before finding an arrow with a note.

Having heard from Christopher Aonuma that he saw a boy who resembled her younger brother named Ewan Amano, Nene Amano is eager to search for Ewan with Mikey Kudo and Christopher searching for him too. However, the Fusion Fighters find Ewan on a bridge and see him with the Bagra Army's Damemon. Shoutmon recognizes Damemon when the Digimon assumes his Tuwarmon form. Ewan and Tuwarmon take their leave with Nene chasing after her younger brother as the bridge is destroyed with Sparrowmon ...

Mikey Kudo, Christopher Aonuma, and Nene Amano arrive in a futuristic kingdom known as Cyber Land. The Fusion Fighters are attacked by an army of Andromon teleported from a flying Whamon. Upon defeating the Andromon, the Fusion Fighters realize their opponents are only puppet replicas as they disable Whamon's teleporter device and learn it is actually an airship. Dorulumon senses a Digimon nearby with the Fusion Fighters finding a strange girl hiding in an airshaft.

Having captured Dorulumon, Splashmon assumes his captive's form to lead an attack on Mikey Kudo, Christopher Aonuma, and Nene Amano. After Splashmon’s MetalTyrannomon are defeated, Splashmon creates a story as Dorulumon to claim he was feigning switching sides to find the Dark General. After Christopher takes his leave, Mikey allows "Dorulumon" to rejoin the Fusion Fighters after his attempt on their lives. Splashmon captures Nene and takes her Fusion Loader.

After landing in the Gold Land, which contains a wide Golden Sea, Mikey Kudo, Christopher Aonuma, and Nene Amano find no traces of the Dark General's flag before a pirate ship rises from underwater. On the pirate ship is the Dark General named Olegmon who is known as the Gold Thief. Olegmon has heard of the Fusion Fighters.

After his crew capture and rewire Ballistamon back into his original state, Olegmon reveals that he created DarkVolumon to aid him. DarkVolumon’s attack somehow traversed him into the Forest Zone, where he was repaired by Shoutmon into Ballistamon. Despite Christopher Aonuma's intervention with Deckerdramon and MailBirdramon, they and OmniShoutmon are all sent flying into the ocean. Olegmon captures Mikey Kudo and enslaves the rest of the Fusion Fighter Digimon.

Mikey Kudo, Christopher Aonuma, and Nene Amano arrive in Canyon Land. The Fusion Fighters find the Dark General named Gravimon who is known as the Earth Spirit. Gravimon has his army of Hippogriffomon, Cerberumon, and Wendigomon stationed around his fortress in preparation for the Fusion Fighters’ arrival.

Though tricked by Gravimon to attack Mikey Kudo and Nene Amano, Christopher Aonuma admits that he would have to confront Mikey even after they defeated Bagramon and his army. Despite Mikey's reluctance to fight, tensions run high as a battle between OmniShoutmon and ZeekGreymon breaks out with OmniShoutmon barely winning as both are loaded into their generals' Fusion Loaders to heal.

Fueled by Deckerdramon's death, Christopher Aonuma's restored bond with Mikey Kudo and Nene Amano allows them to form Shoutmon ×7 and wipe out a majority of Gravimon's army. Though Shoutmon ×7 manages to destroy Gravimon, Gravimon’s hold over Canyon Land is still secure. Hi-VisionMonitamon is sent to investigate Gravimon's castle.

Mikey Kudo, Christopher Aonuma, and Nene Amano arrive to the last kingdom in the Digital World known as Bright Land. The Fusion Fighters start heading towards Bright Land’s tower. Sparrowmon informs the Fusion Fighters that a barrier has prevented her from reaching the top of the tower while finding Bright Land's Digimon that was pinned down to the ground by big spikes. One of the resident Digimon reveals that only the last Dark General named Apollomon can remove them.

Falling into the Digital Underworld below Bright Land, Mikey Kudo, Christopher Aonuma, and Nene Amano find themselves coming to a white castle with a crystal in the middle of the throne room. The crystal projects a hologram of Ewan Amano as he explains the Digital Underworld will be where his army will have a final battle against the Fusion Fighters.

Mikey Kudo ends up facing Ewan Amano in a sword fight before Apollomon Whispered appears. Apollomon Whispered reveals Christopher Aonuma's defeat. Axeknightmon splits into his components once victory is at hand. Axeknightmon and Laylamon have overwhelmed Shoutmon ×5, Beelzemon, and Mervamon. As Apollomon Whispered proceeds to assist Tuwarmon and Axemon against fighting MetalGreymon, Ewan reveals that all he wanted was a world where no one dies.

Christopher Aonuma and Nene Amano search for Ewan Amano. A still wounded Beelzemon joins the search with Mervamon accompanying him. Mikey Kudo and Wisemon are working on a way to leave the Digital Underworld without Mikey or Ewan needing to die. Having been left for dead after Laylamon and Beelzemon gravely wounded each other, Laylamon refuses to accept defeat. Laylamon accepts Apollomon Whispered's offer to force DigiFuse her with Blastmon and the Digital Underworld's energies to assume ...

As SkullKnightmon takes Ewan Amano to the Bagra Army's base, Mikey Kudo, Christopher Aonuma, and Nene Amano know that they have to deal with Apollomon Whispered. Mikey is left with no choice but to destroy Apollomon and Apollomon Whispered together after learning from Wisemon that there is no way to separate the two of them.

After the defeat of all seven Dark Generals, Mikey Kudo, Christopher Aonuma, and Nene Amano head to the Bagra Army's Headquarters named Pandemonia. Bagramon has been expecting the Fusion Fighters to arrive at Pandemonia. Bagramon turns out to be an illusion with Axeknightmon dealing with them.

In Prison Land, the seven Dark Generals defeated Shoutmon ×3 so easily. Moved by the act of sacrificing themselves, Olegmon switches sides to support Mikey Kudo against his former teammates. Apollomon is separated from Apollomon Whispered to settle their own battle. At the same time, Axeknightmon intends not to keep his word to Mikey to spare all his friends. Axeknightmon orders GrandGeneramon to defeat Christopher Aonuma and Nene Amano.

Ewan Amano is captured by Axeknightmon inside the Pandemonia. Ewan’s power is collected by Axeknightmon. Mikey Kudo, Christopher Aonuma, and Nene Amano finally meet Lord Bagra and Axeknightmon outside the palace of Pandemonia. Lord Bagra has already absorbed the Dark Stone. Lord Bagra appears before the Fusion Fighters.

Axeknightmon absorbed his older brother who is known as Lord Bagra in a forced DigiFusion. Axeknightmon reveals that he unsealed the Darkness Loader. Axeknightmon used Nene Amano and Ewan Amano to overthrow Lord Bagra. Axeknightmon wants to become the new ruler of the Digital World. Mikey Kudo managed to rescue Ewan from the enlarged Tyutyumon.

Mikey Kudo, Christopher Aonuma, Nene Amano, Ewan Amano, Angie Hinomoto, and Jeremy Tsurgi are transported back to Earth by the DigiMemories of Examon and WarGreymon. Examon reveals Lord Bagra's plan. Examon also reveals the forming of all the DigiMemories. Ewan's Darkness Loader is transformed into a yellow Fusion Loader. Examon and WarGreymon's DigiMemories revive Omnimon's DigiMemory. A decisive battle begins between the Fusion Fighters United Army and the Bagra Army.