User:FinnishPokéFan92/Naruto: Johto Journeys

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Naruto: Johto Journeys is a fanfiction written by the username KitsuneDragon at Fanfiction.net. The fanfiction contains elements from Pokémon and Naruto, both of which are popular series originating from Japan. The fanfiction contains the locations of the Pokémon world, but mostly replaces the characters with those from Naruto. The events of this fanfiction are mostly based on those from Pokémon HeartGold and SoulSilver, but it also takes influence from other Pokémon games, the Pokémon anime, and the Pokémon Adventures manga, among other things. The readers of the story could influence several elements of the story (including Hinata's Eevee's evolution) by voting. This page lists the notable events of this fanfiction.

Although this fanfiction is now completed, KitsuneDragon has promised to write a sequel to the story, based on the plot of Pokémon Omega Ruby and Alpha Sapphire.

Major events

Round	Details
Chapter 1: In the Beginning	30 years earlier: A youth from Pallet Town receives a Pokédex and a Pikachu from Professor Sarutobi and starts his Pokémon journey, aiming to complete the Pokédex and become the Pokémon League Champion. The youth defeats the eight Kanto Gym Leaders, earning the eight necessary Badges to enter the Indigo Plateau Pokémon League. The youth defeats the evil organization ROOT, along with its leader, Danzo. The youth confronts his rival, A, at the Pokémon League and defeats him, becoming the new Pokémon League Champion. A boy named Naruto Uzumaki goes asleep on the eve of his 12th birthday, when he will be able get his starter Pokémon and start his own journey.
Chapter 2: First Steps	The youth of New Bark Town, including Naruto, receive their respective starter Pokémon from Professor Iruka: Naruto starts with a Cyndaquil. Sakura Haruno starts with a Chikorita. Sasuke Uchiha starts with a Totodile. Ino Yamanaka starts with a Sunkern. Shikamaru Nara starts with a Stantler. Chouji Akimichi starts with a Caterpie. Kiba Inuzuka starts with a Growlithe nicknamed "Akamaru". Shino Aburame starts with a Spinarak. Hinata Hyuga starts with an Eevee. All starting Trainers also receive their Pokédexes. Naruto starts his journey, accompanied by Hinata. Professor Iruka sends Naruto and Hinata to deliver him an item from Mr. Pokémon on Route 30. Naruto and Hinata meet Professor Sarutobi. Naruto has his first battle with Sasuke and wins. Naruto and Hinata deliver a Pokémon Egg from Mr. Pokémon to Professor Iruka. Professor Iruka suggests Naruto and Hinata head to Violet City, where there's a Gym, and a Contest will be held in two days. Naruto catches his first Pokémon, a Pidgey. Hinata catches her first Pokémon, a Sentret.
Chapter 3: Triumph and Loss	Naruto and Hinata have a Multi Battle against Youngsters Timmy and Tommy and win. Naruto's Cyndaquil learns Ember. Hinata catches a Caterpie. Naruto catches a Rattata, a Weedle, a Caterpie, a Spinarak, and a Sentret. Naruto and Hinata arrive in Violet City. Hinata registers herself as a Pokémon Coordinator. Naruto's Cyndaquil learns Quick Attack. Naruto's Weedle and Caterpie evolve into Kakuna and Metapod, respectively. Naruto's Cyndaquil evolves into Quilava. Naruto challenges the Sprout Tower and wins, earning TM70 (Flash) from Elder Li as a reward. Naruto challenges the Violet Gym's Gym Leader, Shinno, and wins, earning the Zephyr Badge and TM51 (Roost). Hinata participates in her first Pokémon Contest in Violet City, but is defeated by Sakura in the semifinals. Ino wins the Violet City Pokémon Contest, earning her first Ribbon. Naruto decides to head to Azalea Town. Naruto meets up with Kiba again.
Chapter 4: The ROOT of all Evil	Naruto has a battle with Kiba and wins. Naruto and Hinata receive a Pokémon Egg each, sent to them by Professor Iruka. Hinata's Caterpie is revealed to have evolved into Metapod. Hinata's Metapod evolves into Butterfree and learns Confusion. Naruto catches a Mareep. Naruto and Hinata each receive an Old Rod from Fisherman Roy. Hinata's Butterfree learns Sleep Powder and Poison Powder. Naruto and Hinata each catch an Ekans, a Bellsprout, a Hoppip, a Wooper, a Magikarp, a Tentacool, a Geodude, an Onix, and a Sandshrew, while Hinata also catches her own Mareep. Naruto and Hinata meet Hiker Akatsuchi Miyake. Naruto and Hinata encounter ROOT for the first time.
Chapter 5: You're Bugging Me	Naruto and Hinata meet Kurt. Naruto and Hinata save the Slowpoke of the Slowpoke Well from ROOT. Naruto catches one of the Slowpoke. Naruto challenges the Azalea Gym. During his challenge, Naruto catches a Pineco and a Heracross. Naruto's Quilava's Blaze activates for the first time. Naruto's Pidgey evolves into Pidgeotto. Naruto battles the Azalea Gym's Gym Leader and Shino's father, Shibi Aburame, and wins, earning the Hive Badge and TM89 (U-turn).
Chapter 6: Look Underneath the Underneath	Naruto and Hinata learn that a Pokémon Contest is going to be held in Goldenrod City. Akatsuchi joins Naruto and Hinata. Naruto meets up with Sasuke again. Akatsuchi meets Sasuke for the first time. Sasuke is revealed to have caught a Gastly and a Zubat, while his Totodile has evolved into Croconaw. Naruto's Quilava is revealed to have learned Flame Wheel. Naruto and Sasuke have a battle, which ends in a draw declared by Sasuke. Naruto, Hinata, and Akatsuchi receive a Fast Ball, a Love Ball, and a Heavy Ball, respectively, from Kurt. Akatsuchi is revealed to own a Geodude. Hinata receives the HM01 (Cut) from Charcoal Maker Sumi for catching his Farfetch'd. Naruto and Hinata see Celebi in the Ilex Forest. Hinata catches a Poliwag. The group meets Kakashi Hatake. Naruto and Hinata battle Kakashi together, but are defeated. Naruto and Hinata's Eggs hatch into Dratini and Togepi, respectively.
Chapter 7: Fool's Goldenrod	Naruto and his friends arrive in Goldenrod City. Naruto wins an Abra at the Goldenrod Game Corner. Naruto challenges the Goldenrod Gym's Gym Leader, Fuka, but loses by forfeit. The group meets up with Kakashi again. Kakashi is revealed to be a member of the Johto Elite Four. Kakashi agrees to help Naruto in his training.
Chapter 8: I Rise with the Sun	Naruto trains with Kakashi. Naruto leaves his Dratini in the Pokémon Day Care. Hinata is revealed to have taught her Sentret Hyper Beam via TM15. Hinata catches a Nidoran♀. Hinata's Sentret evolves into Furret. Hinata meets up with Sakura and Ino again. Naruto's Mareep is revealed to have evolved into Flaaffy during his training. Naruto is revealed to have caught a Nidoran♂ during his training. Naruto challenges Fuka to a rematch and wins, earning the Plain Badge and TM45 (Attract). Ino is revealed to have caught an Oddish. Sakura is revealed to have caught a Marill. Hinata is revealed to have taught her Eevee Focus Blast via TM52. Hinata meets Wallace, a fellow Coordinator. Hinata's Eevee evolves into Espeon. Hinata wins the Goldenrod Pokémon Contest, earning her first Ribbon. The next Contest is revealed to be held in Olivine City. Naruto learns that the next Gym is located in Ecruteak City. Wallace is revealed to be a member of ROOT.
Chapter 9: I look Good in Black	Ruby and Sapphire, two other members of ROOT, are introduced. ROOT is revealed to have taken over the Goldenrod Radio Tower. ROOT is revealed to have their HQ in Mahogany Town. Akatsuchi is revealed to own a Zubat, an Onix, and a Sandshrew. ROOT attacks the Pokéathlon Dome to steal a rare Shiny Vulpix. Although Naruto and his friends interfere with their actions and several ROOT members are caught by the police, the Shiny Vulpix still gets stolen and delivered to ROOT's HQ. Naruto's Wooper learns Mud Bomb. Wallace, Ruby, and Sapphire are revealed to be children of ROOT's new leader.
Chapter 10: Ghosts of the Past	Naruto, Hinata, Shino, and Kiba enter the Bug-Catching Contest and receive five Net Balls each to be used during the contest. Naruto catches a Beedrill and a Scyther during the Bug-Catching Contest. Hinata catches a Pinsir during the Bug-Catching Contest. Akatsuchi catches the Sudowoodo blocking Route 36. Naruto and Hinata tie for the first place in the Bug-Catching contest, receiving a Leaf Stone and a Moon Stone, respectively, as prizes. Naruto's Wooper evolves into Quagsire. Akatsuchi's Sandshrew and Geodude evolve into Sandslash and Graveler, respectively. Akatsuchi temporarily trades his Graveler for Hinata's Nidoran♀, allowing it to evolve into Golem. Akatsuchi temporarily trades his Sandslash to Hinata, allowing her to register its information to her Pokédex. The group arrives in Ecruteak City. Naruto challenges the Ecruteak Gym. During his challenge, Naruto finds TM30 (Shadow Ball). Naruto's Pidgeotto is revealed to have learned Twister. Naruto battles the Ecruteak Gym Leader, Kurenai Yuhi, and wins, earning the Fog Badge. The group learns of the legend of Ho-Oh and Lugia. Naruto meets up with Sasuke again. Naruto, Sasuke, and Hinata encounter Raikou, Entei, and Suicune at the Burned Tower.
Chapter 11: BURN! FLAMES OF YOUTH!	Sasuke tries to battle Entei, but it escapes along with the other legendary beasts. Hinata turns 12 and receives a Twisted Spoon from his father as a gift, giving it to her Espeon to hold. Naruto and his friends encounter ROOT again. Naruto receives HM03 (Surf) from an old man for saving two Kimono Girls from ROOT at Ecruteak's Kimono Dance Theater. Naruto teaches Surf to Quagsire. Naruto receives an Eevee contained in a Luxury Ball from an unknown person via Professor Iruka. Hinata catches a Miltank, a Snubbull, a Meowth, and a Farfetch'd. Naruto catches a Tauros, an Exeggcute, a Magnemite, and a Ledyba. Naruto and his friends meet Rock Lee. The group helps out a sick Miltank at the Miltank Ranch. The group arrives in Olivine City. Hinata's Hoppip is revealed to have evolved into Skiploom. Naruto and his friends meet Tenten. Naruto and Lee depart for Cianwood City to get medicine ingredients for Amphy.
Chapter 12: Fighting Spirit, Iron Will	On the way to Cianwood, Naruto encounters Suicune again. Naruto finds the Silver Wing. Naruto and Lee arrive in Cianwood City, where Naruto encounters Suicune and Raikou once again. Raikou, Suicune, and Entei show Naruto, Hinata, and Sasuke respectively a vision of the future, where ROOT attacks the Silver Conference. Naruto and Lee deliver the medicine ingredients to the Glitter Lighthouse. Hinata mixes a medicine to cure Amphy. The group meets up with Sasuke and Sakura again. Sakura's Chikorita is revealed to have evolved into Bayleef. Lee and Tenten are revealed to be the Gym Leaders of Cianwood and Olivine Gyms, respectively. Sasuke is revealed to have caught a Sneasel. Naruto's Pidgeotto evolves into Pidgeot. Naruto and Sasuke have a Multi Gym Battle against Lee and Tenten and win, earning the Storm and Mineral Badges for both of them. Naruto's Quilava and Sasuke's Croconaw evolve into Typhlosion and Feraligatr, respectively.
Chapter 13: Through the Eyes of a Pokemon	Naruto and Sasuke are revealed to have earned a TM23 (Iron Tail) and a TM01 (Focus Punch) each for winning their battle against Tenten and Lee. Hinata is revealed to have taught her Espeon Shadow Ball via Naruto's TM30. Hinata's Espeon learns Psybeam. Hinata wins the Olivine City Pokémon Contest, earning her second Ribbon.
Chapter 14: Red Gyarados	Naruto and Sasuke's groups head to Mahogany Town together. Naruto's Flaaffy is revealed to have evolved into Ampharos during a rematch with Lee and Tenten. Akatsuchi is revealed to have evolved his Onix into Steelix by temporarily trading it with Naruto while holding a Metal Coat received from Tenten. While traveling through Route 42, the group encounter the legendary beasts again. The group follows the legendary beasts through Mt. Mortar. Naruto catches a Machop. Hinata catches a Marill and an Aipom. The group arrives in Mahogany Town. The group meets Haku. Naruto, Sasuke, and Hinata head to the Lake of Rage to investigate the actions of ROOT. Naruto, Sasuke, and Hinata each catch a Girafarig, a Venonat, and a Noctowl. The trio encounters a mysterious cloaked figure, who tells them about the Red Gyarados. The trio battles the Red Gyarados at the Lake of Rage. Naruto's Ampharos is revealed to have learned ThunderPunch. The leader of ROOT orders the trio and the Red Gyarados be brought to the ROOT HQ.
Chapter 15: The Belly of the Beast	Naruto, Sasuke, and Hinata are captured by ROOT via an artificial whirlpool. The trio meets the leader of ROOT for the first time. The trio escapes from their cage with a stolen Card Key. Twenty minutes earlier, Sakura and Akatsuchi meet the mysterious cloaked man in Mahogany Town. The cloaked man, along with Sakura and Akatsuchi, infiltrate ROOT's headquarters. Sakura is revealed to have won a Porygon at the Goldenrod Game Corner. Sakura and Akatsuchi find out about ROOT's "Project Danzo" and "Project Time Travel". Sakura's Marill evolves into Azumarill. Sakura and Akatsuchi reunite with Naruto, Sasuke, and Hinata. The group recovers the stolen Shiny Vulpix. Hinata's Skiploom and Nidoran♀ are revealed to have evolved into Jumpluff and Nidorina, respectively. Naruto and Sasuke each catch an Electrode. The group confronts Ruby, Sapphire, and Wallace. Ruby, Sapphire, and Wallace remove the Everstones from their Charmander, Bulbasaur, and Squirtle, causing them to immediately evolve into their final stages. Naruto, Sasuke, and Sakura battle Ruby, Sapphire, and Wallace while Hinata and Akatsuchi escape. During the battle, Sakura's Bayleef evolves into Meganium.
Chapter 16: Pandemonium	Naruto, Sasuke, and Sakura continue their battle with Ruby, Sapphire, and Wallace, but the ROOT trio ends up retreating. ROOT's leader briefly battles the cloaked man before escaping with Ruby, Sapphire, and Wallace, while the remaining Electrode in the generator room Self-Destruct, destroying the ROOT HQ. Haku is revealed to be the Gym Leader of Mahogany Gym. The cloaked man is revealed to be Izuna Uchiha, the current Pokémon League Champion. The contents of ROOT's "Project Danzo" and "Project Time Travel" are fully revealed. Hinata admits her feelings to Naruto.
Chapter 17: Glacier Badge	Sasuke is revealed to have caught a Ponyta, an Electabuzz, and a Rhyhorn, while his Gastly has fully evolved into Gengar. Sasuke battles Haku, but is defeated. Sakura is revealed to have caught a Jigglypuff, a Vulpix, and a Pikachu. The group and their Pokémon train with Haku in preparation for the Gym battle and facing ROOT in Goldenrod. During the training session, multiple Pokémon evolve: Naruto's Eevee evolves into Umbreon. Sasuke's Ponyta and Rhyhorn evolve into Rapidash and Rhydon, respectively. Sakura evolves her Porygon into Porygon2 with an Up-Grade she found from the former ROOT HQ. Akatsuchi's Zubat evolves into Golbat. Hinata uses her Moon Stone to evolve her Nidorina into Nidoqueen, while her Togepi evolves into Togetic*. Sasuke is revealed to have caught the Red Gyarados while being sucked into the ROOT HQ. Naruto and Sasuke have a Double Gym Battle against Haku and win, earning the Glacier Badge and a TM07 (Hail) for both of them. The group and Haku prepare to head to Goldenrod City to face ROOT.
Chapter 18: Top Floor Please	ROOT is revealed to have taken over Goldenrod City. Naruto, his friends, and Izuna start their plan against ROOT. Naruto and Hinata encounter Wallace in the Underground. Wallace is revealed to own a Scizor, a Muk, and an Ursaring. Hinata battles Wallace to buy time for Naruto. Naruto saves ROOT's hostages from the Underground. Naruto encounters a mysterious man. Sasuke, Sakura, Akatsuchi, Haku, and Izuna storm the Goldenrod Radio Tower. Sakura encounters Sapphire on 3F, and starts a battle with her. Sapphire is revealed to own an Arcanine, a Hitmonlee, and a Wobbuffet. Sasuke battles Ruby on 4F. Ruby is revealed to own a Skarmory, a Magneton, and a Golem. Izuna encounters ROOT's leader, Nagato Uzumaki, on 5F, and starts a battle with him.
Chapter 19: Dance with the Devil	Sapphire is revealed to own a Kangaskhan and a Sandslash. Sakura defeats Sapphire. Naruto is revealed to own HM02 (Fly). Sasuke defeats Ruby. The man Naruto encountered is revealed to be Jiraiya. Jiraiya is revealed to be Naruto's godfather. Naruto meets Professor Sarutobi again. Hinata defeats Wallace. Wallace reveals that Nagato is planning to use Celebi to bring back Konan, the dead mother of Nagato's children. Izuna battles Nagato, but Nagato ends up escaping with his children before being defeated, thus bringing the battle against ROOT to its end.
Chapter 20: The Ultimate Moves	In Mahogany Town, week after the battle with ROOT, Jiraiya tells the group a story of his three former students; Nagato, Konan, and Yahiko. Jiraiya's story makes Hinata realize that Nagato is the leader of ROOT. Haku takes care of the Shiny Vulpix until its Trainer, Shizuka, arrives. Jiraiya gives Akatsuchi a Hard Stone. Akatsuchi's Golbat is revealed to have evolved into Crobat. Jiraiya gives Hinata a Shiny Stone, which she uses to evolve her Togetic into Togekiss. Hinata teaches Togekiss Fly via Naruto's HM02. Jiraiya gives Naruto, Sasuke, and Sakura each one of Kimberly's bracelets. Naruto, Sasuke, and Sakura's starter Pokémon learn their respective ultimate moves; Blast Burn, Hydro Cannon, and Frenzy Plant, although not perfected. Sakura and Hinata leave the group and head to Ecruteak City to participate in a Pokémon Contest held there. Akatsuchi leaves the group to go training at the Ruins of Alph. Naruto and Sasuke head to Blackthorn City. At the Route 34 Day Care, Naruto's Dratini evolves into Dragonair and leaves to reunite with its Trainer.
Chapter 21: Blackthorn City, The Birthplace of Uchiha	Naruto and Sasuke are revealed to have obtained a Good Rod each. Naruto and Sasuke each catch a Lickitung, a Tangela, an Aipom, and a Remoraid. Naruto and Sasuke enter the Ice Path. Naruto and Sasuke each catch a Delibird, a Jynx, and a Swinub. While traveling through the Ice Path, Naruto and Sasuke encounter two Kimono Girls. The Kimono Girls give Naruto and Sasuke HM07 (Waterfall). The Kimono Girls also give Naruto the Rainbow Wing, while Sasuke is given the Clear and Tidal Bells. Naruto and Sasuke arrive in Blackthorn City. Naruto's newly evolved Dragonair returns to him. Naruto challenges the Blackthorn Gym's Gym Leader and Sasuke's mother, Mikoto Uchiha, and wins. Naruto's Typhlosion masters Blast Burn.
Chapter 22: The Negatives of Rivalry	Sasuke challenges Mikoto to a Gym battle, but is defeated. Naruto learns about Itachi, Sasuke's missing older brother. Sasuke challenges Naruto to a battle.
Chapter 23: Itachi Uchiha	Naruto and Sasuke have a battle, which ends in a draw. Naruto learns Itachi's story from Mikoto.
Chapter 24: Legendary Pokemon Pt 1	Sasuke has a rematch with Mikoto and wins. Sasuke's Feraligatr is revealed to have mastered Hydro Cannon. Mikoto refuses to hand out the Rising Badge to Naruto and Sasuke until they clear the Elder's test at the Dragon's Den. Naruto is revealed to have obtained HM05 (Whirlpool) from Izuna after defeating ROOT in Mahogany Town. Naruto and Sasuke pass the Elder's test and receive a Rising Badge and a TM58 (Dragon Pulse) each from Mikoto, thus completing their requirements for the Pokémon League. Hinata and Sakura are both revealed to have earned their fourth Ribbons. The Pokémon League Conference is revealed to start in three months. The Kimono Girls appear. The Kimono Girls take Naruto to Ecruteak City to confront Ho-Oh at the Bell Tower. Sasuke borrows Mikoto's Charizard to fly him to Cianwood City to confront Lugia at the Whirl Islands. Sasuke meets up with Hinata again. Hinata is revealed to have caught a Lapras in the Union Cave. Sasuke and Hinata confront Lugia. Naruto meets up with Sakura again. Naruto and Sakura confront Ho-Oh.
Chapter 25: Legendary Pokemon Pt 2	ROOT is revealed to be building a new base at the Tohjo Falls. With "Project Danzo" having failed, Nagato orders "Project Time Travel" to be started. Nagato sends his admins to capture Ho-Oh and Lugia. Sasuke and Hinata battle Lugia, but are defeated. Naruto and Sakura battle Ho-Oh, but are unable to defeat it. Naruto attempts to catch Ho-Oh, but fails. ROOT admins successfully catch Lugia and Ho-Oh, and bring them back to their base. ROOT is revealed to have kidnapped Kurt. Nagato forces Kurt to start creating the GS Ball.
Chapter 26: The Path of Victory	In the Ecruteak City Pokémon Center, Naruto wakes up from a two-day state of unconsciousness following the battle with Ho-Oh. Naruto, Sasuke, Hinata, and Sakura reunite. Sasuke and Hinata are revealed to have been rescued by Entei and Suicune. Naruto admits his feelings to Hinata. Naruto and Hinata have their first kiss. The Grand Festival is revealed to be held in one month. Naruto and Sasuke depart to New Bark Town to head to the Pokémon League from there. Naruto and Sasuke go through the Victory Road. Naruto and Sasuke each catch an Ursaring and a Donphan. Naruto and Sasuke arrive at the Indigo Plateau and prepare to sign up for the Pokémon League.
Chapter 27: The Fifth Ribbon	Sakura and Hinata enter the Ecruteak City Pokémon Contest. The Grand Festival is revealed to be held in two weeks. Sakura and Hinata tie for the first place of the Contest. The Ecruteak Ribbon is split in half, giving both Sakura and Hinata their fifth Ribbons and thus completing their requirements for the Grand Festival. The Grand Festival is revealed to be held at the Indigo Plateau before the start of the Pokémon League Conference.
Chapter 28: The Grand Festival	At the Indigo Plateau, Sakura and Hinata register for the Grand Festival. Chouji's Caterpie is revealed to have fully evolved into Butterfee. Ino's Sunkern is revealed to have evolved into Sunflora. Sakura is revealed to have evolved her Pikachu, Vulpix, and Jigglypuff into Raichu, Ninetales, and Wigglytuff, respectively. Sakura tells Hinata about the Kalos region. Naruto learns that the Grand Festival will be held at the Indigo Plateau. Hinata's father, Hiashi Hyuga, arrives to take his daughter back to Saffron City. Hinata makes a bet with her father: if she manages to impress him in the Battle Rounds, he will let her continue being a Coordinator. But if not, she will have to come with him to Saffron City to become a Gym Leader. The Grand Festival begins. Chouji is revealed to have caught a Mamoswine. The first half of the Appeal Round is conducted.
Chapter 29: Don't Look Down on Me	Sakura, Hinata, Ino, and Chouji all pass the first half of the Appeal Round. Chouji is revealed to have caught a Tauros. Ino is revealed to have caught a Teddiursa. Sakura, Hinata, Ino, and Chouji all pass the second half of the Appeal Round, qualifying themselves for the Battle Rounds. The first battle is revealed to be between Ino and Chouji.
Chapter 30: Rising through the Ranks	Chouji is defeated by Ino, thus eliminating him from the tournament. At the ROOT base, Kurt is forced to continue his work on creating the GS Ball. Sakura and Hinata win their first battles. Sakura defeats Sasako Fuuma, advancing to the next round. Ino is defeated by Hikari Nonaka, eliminating her from the tournament and placing her in Top 8. Hinata defeats Diana Prince, advancing to the next round
Chapter 31: Bringing Down the House	Akatsuchi returns. Akatsuchi is revealed to have caught multiple Unown at the Ruins of Alph. Naruto, Sasuke, Hinata, and Sakura each receive an Unown from Akatsuchi, sent for them to Professor Iruka's laboratory. Akatsuchi gives Naruto and Sasuke each an Old Amber. Akatsuchi gives Naruto and Sasuke a choice between the Dome and Helix Fossils. Although both of them want the Dome Fossil, Naruto eventually claims it, leaving Sasuke with the Helix Fossil. The semifinals of the Grand Festival begin. Sakura is defeated by Sora Yasuharu, eliminating her from the tournament and placing her in Top 4. Hinata defeats Hikari, advancing to the finals. Hinata is defeated by Sora in the finals, making her the runner-up.
Chapter 32: Aftermath	Sora is awarded with the Ribbon Cup. Despite Hinata's loss, Hiashi still decides to let her continue her career as a Pokémon Coordinator. The Grand Festival ends. On the top of Mt. Silver, the Trainer who left Pallet Town 30 years previously is looking for Mew.
Chapter 33: The Wrath of God	The GS Ball is finished. Nagato kills Kurt. Kiba is revealed to have evolved his Growlithe, Akamaru, into Arcanine. The opening ceremony of the Silver Conference is interrupted by ROOT, just as the legendary beasts had envisioned. ROOT launches an attack across the Kanto-Johto continent. Ho-Oh and Lugia attack the Indigo Plateau. The ROOT war begins. The legendary beasts arrive to assist in the battle. The legendary beasts join Naruto and his friends, registering their info in their Pokédexes. Naruto, his friends, and the legendary beasts start pursuing Ho-Oh and Lugia. Naruto's Dragonair is revealed to have evolved into Dragonite*.
Chapter 34: Battle of the Gods	The Pallet Town Trainer and Naruto's father, Minato Namikaze, retrieves Kushina's Moltres from Mt. Silver, while Kushina retrieves Minato's Articuno from the Seafoam Islands and his Zapdos from the Power Plant. Minato and Kushina head to the Ilex Forest to help Naruto. Nagato and his children, followed by Naruto and his friends, arrive in the Ilex Forest. Naruto's Typhlosion is revealed to have learned ThunderPunch. Naruto, Sasuke, and Sakura battle against Ruby, Sapphire, and Wallace, but their combined finishing blow is blocked by Nagato's Alakazam's Protect. The legendary beasts battle against Ho-Oh and Lugia, but are defeated. Minato and Kushina arrive to help with the legendary birds. Minato reveals the group that he is Naruto's father.
Chapter 35: The Fallen God	Naruto finds out that he is Nagato's cousin, and thus also related to Ruby, Sapphire, and Wallace. Minato and Kushina battle against Ho-Oh and Lugia. Hinata and Sakura heal the legendary beasts. Minato takes Naruto with him to Cerulean Cave. Minato tells Naruto the story of Mewtwo and how he battled it once, but was forced to retreat. Minato is revealed to own the Master Ball, which he received from the president of Silph Co. 30 years earlier. Naruto and Minato confront and battle Mewtwo, eventually managing to defeat it. Naruto manages to convince Mewtwo to become his comrade. Naruto catches Mewtwo with the Master Ball.
Chapter 36: Judgement of the Gods	Hinata, Akatsuchi, and Kushina are almost crushed to death by Ho-Oh and Lugia's Extrasensory attacks, but are saved by Naruto and Minato. Mewtwo battles against Nagato and defeats him. Before Mewtwo can kill Nagato, Celebi appears from the Ilex Forest shrine. Nagato catches Celebi with the GS Ball. Nagato and his children enter the time stream through the shrine. With the aid of the legendary beasts and birds, Mewtwo successfully destroys the control collars on Ho-Oh and Lugia. Naruto and Sasuke catch Ho-Oh and Lugia, respectively. Because only the legendary beasts can enter the time stream, only Naruto, Sasuke, and Hinata pursue Nagato and his children into it. Naruto, Sasuke, and Sakura battle against Nagato in the time stream. Ruby, Sapphire, and Wallace protect their father from Raikou's Thunder attack, getting severely injured in the process. Naruto and Raikou pursue Nagato through time, ending up 13 years in the past in the Viridian Forest. Naruto takes Celebi from Nagato. When Nagato resists trying to be pulled back into the time stream, Raikou accidentally shocks him to death.
Chapter 37: After the Fall	A month after the end of the ROOT war, Sasuke, Sakura, Hinata, and Naruto go over their war traumas with their parents. It is revealed that Minato was the one who sent Naruto his Eevee. Minato explains Naruto how the Pokémon League Association works. Minato tells Naruto and Kushina why he has been absent for twelve years. Minato reveals that he was in a two-year coma following his battle with Mewtwo. Naruto tells Ruby, Sapphire, and Wallace the details of what happened to Nagato. Ruby, Sapphire, and Wallace are adopted into the Uzumaki family. Naruto and Sasuke free Ho-Oh, Lugia, Celebi, and the legendary beasts, although they still choose to remain under their ownership. Naruto reveals that he is going to keep Mewtwo for himself.
Chapter 38: To Be a Master	Naruto is revealed to have completed his Pokédex, excluding Mew from the "caught" section. Seven months after the end of the ROOT war, the Silver Conference restarts at the rebuilt Indigo Plateau. Sasuke is revealed to have caught a Nidoking, an Arbok, and a Hypno. Sasuke wins his Screening Round battle against Shigery Okido, advancing to the next round. Kiba is revealed to have caught a Jolteon, a Flareon, and an Umbreon. Kiba wins his Screening Round battle against Hazuki Toriumi, advancing on to the next round. Shino is revealed to have caught two Pineco and a Forretress. Shino wins his Screening Round battle against Tsukushi Ishikawa, advancing on to the next round. Naruto is revealed to own a Venusaur, a Blastoise, and a Charizard. Naruto wins his Screening Round battle against Shinji Furushima, advancing to the next round.
Chapter 39: Make it Double	Shino is revealed to have caught a Pinsir. Shino wins his Double Battle against Hayato Sora. Naruto is revealed to have revived his Old Amber and Dome Fossil into an Aerodactyl and a Kabuto, respectively, the latter which has evolved into Kabutops. Minato is revealed to have helped Naruto in his training after the war. Naruto wins his Double Battle against Satoshi Taijiri. Sasuke is revealed to have revived his Old Amber into an Aerodactyl as well, while his Helix Fossil was revived into an Omanyte, which has evolved into an Omastar. Sasuke wins his Double Battle against Tetsuya Nojima. Kiba wins his Double Battle against Matis.
Chapter 40: The Big Leagues	Out of the 132 remaining Trainers, the Pokémon League chooses the best 16 to advance to the next round, including all the New Bark Town Trainers. Kiba is revealed to have caught a Granbull and a Houndoom. Naruto defeats Kiba, advancing to the quarterfinals. Shino defeats Haruka Safaia, advancing to the next round. Sasuke defeats Shizuka Remei, advancing to the quarterfinals.
Chapter 41: Finding a Purpose	Sasuke wins his quarterfinal battle against Kikuko Sugiyama, advancing to the semifinals. Shino is revealed to have caught a Heracross and a Scizor, while his Spinarak has evolved into Ariados. Shino is defeated by Ryuu, eliminating him from the Silver Conference and placing him in Top 8. Naruto wins his quarterfinal battle against Gaara, a former member of Cipher, advancing to the semifinals
Chapter 42: One More Step up the Ladder	Sasuke defeats Satoshi Taijiri in the semifinals, advancing to the finals. Naruto defeats Ryuu in the semifinals, advancing to the finals.
Chapter 43: Settling the Score	Naruto defeats Sasuke in the finals, making him the winner of the Silver Conference and giving him the right to challenge the Elite Four.
Chapter 44: The Elite Four Pt 1	Naruto starts his Elite Four challenge. Naruto defeats Neji Hyuga, the first member of the Elite Four Naruto defeats Orochimaru, the second member of the Elite Four. Naruto advances to the third room.
Chapter 45: The Elite Four Pt 2	Naruto defeats Maito Gai, the third member of the Elite Four. Naruto ties with Kakashi, the final member of the Elite Four, but since he beat all of Kakashi's Pokémon, he is still declared victorious, thus allowing him to challenge Izuna for the title of the Champion.
Chapter 46: Johto Photo Finish	Naruto battles Izuna for the title of the Champion, but is defeated. Two months lates, Naruto leaves his home to train with his parents, leaving Ruby, Sapphire, and Wallace in charge of their house while they're away. At the Pokémon League, Izuna receives intel from Jiraiya from Hoenn, regarding the increased actions of Team Magma and Team Aqua.