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(Just before we start I don't want to see any whiney comments, the manga is great and one of the best stories out there today but like most people, I don't think it's perfect. This is no hate on Kishimoto, but here is how I would've made alterations to Naruto Shippuden, please enjoy.)
ARC #1 - RESCUE THE KAZEKAGE
In my opinion this arc could be improved on the most, lots of potential.
MAIN VILLAIN: Deidara & Sasori
-The show instead of starting with a Sasuke flash forward actually shows a glimpse forward to the mid-point of the series, and shows a mysterious shady figure destroying Konoha- we see an obscured Sage Naruto summoned with the boss toads. Cut to black.
[video=youtube;CyMqS99jXNQ]https://www.youtube.com/watch?v=CyMqS99jXNQ[/video]
-Back in modern day, Naruto returns to the village (with actual new jutsu and techs) after the 3 years with Jiraiya only to find out that things in Konoha are very different. The usual K11 gang have grown apart and actively avoid each other after the Sasuke incident, Shikamaru got everybody almost killed and thus there's problems between them. Naruto obviously tries to fix this but is roped into doing the bell test against Kakashi (which is a real but light-hearted fight to showcase how strong Sakura & Naruto have actually become (like Ninja Storm 2 boss fight)
-Gaara is kidnapped by Deidara and Tsunade sends the K11 as one big unit to deal with the global affair led by Kakashi. Because of their bad teamwork they split into groups, Team 8 tracking, Team InoShikaCho VS Sasori instead of Kankuro etc.
-The villains of this arc are Sasori and Deidara. No members die in this first arc. After being defeated in their 1v1s and getting Gaara stolen back (how it happened in the OG manga) they decide to go big and take the Sand Village by seige, using both Deidara's dragon and Sasori's 100 Puppets. This traps the K11 in the Sand Village and forces them to work together thanks to Naruto's leadership. They protect each other and become allies again, showing Naruto has brought them back together- eventually Gaara awakes and finishes them, forcing them to retreat.
-At the end of the arc as they return Hidan & Kakazu appear to the defeated 2 and tell them news that Itachi Uchiha and Kisame Hoshigaki have gone rogue from the Akatsuki and need to be hunted down.
TENCHI BRIDGE ARC:
MAIN VILLAIN: Orochimaru and the Sound Village
This arc is mostly perfect, personally I would make Sai more powerful to make him more relevant for future arcs and more mystery surrounding Orochimaru and Sasuke, even so far as to venture into the 'Sound Village'.
This arc is basically the existing one mixed with the House of Orochimaru! filler from part 1. We get to see more of The Sound Village and fight Kabuto & Oro at the bridge, Oro's experiments and Kimimaro (who is still alive cough COUGH) and finally at the end Sasuke, who Naruto, Sai & Sakura properly fight together. This fight is more like the Storm 2 fight and it ends with Oro stopping Sasuke from killing them with Kirin, stating he wants them alive.
HIDAN & KAKAZU ARC
This arc is pretty much perfect already, Hidan dies, the only big change is that KAKAZU IS NOT KILLED. HE ESCAPES.
HEBI FORMATION ARC
MAIN VILLAIN: Kimimaro and Itachi
Much like the original arc except more dramatic and a self-contained story. Sasuke has a real fight with Orochimaru and recruits the 3, all agreeing to help each other fulfill their own goals. Jugo wants to cure his disease & be controlled, Suigetsu wants to collect the swords of the Mist and Karin wants freedom and to kill the man who butchered her mother, Kimimaro Kaguya (a better goal than getting laid) whilst Sasuke's goal is to still to get revenge on Itachi.
Jugo is kept under control by Sasuke, Sui goes to Zabuza's grave and gets the sword and Karin starts (genuinely) falling for Sasuke. All whilst being followed by Kimimaro. Hebi VS Kimimaro but instead of killing Kimi, Karin decides to move on with her life and let him go, whilst still refusing to forgive him. Sasuke sees this & thinks about his own drive. Meanwhile through all of this Naruto is learning more jutsu
Sasuke slowly starts to remember the closeness of being in a group and is reminded of Team 7. He shows signs through this arc of slowly regaining his humanity, even showing slight interest in the (SWEET AND SMART AND NOT CREEPY) Karin, finally showing signs of being able to move on with his life when Deidara and Tobi appear, telling him that his brother has gone rogue, triggering Sasuke's lust again and giving him a reason to join the Akatsuki.
THE WILL OF FIRE ARC
MAIN VILLAIN: Hiruko
This arc is the plot of Naruto movie 3. I know this seems random and kinda dumb but this film is actually fantastic and does a lot for character development, fitting in perfectly with the Naruto storyline. Kakashi hasn't been seen for a while in this version (since the Hidan&Kakazu arc) and so this arc is mainly about him and Naruto.
The missing nin Hiruiko (old friend of the Sannin) tries to bring about the end of the world, Kakashi lets himself be controlled and goes to them to sacrifice himself for the sake of the village. Naruto and Sakura are locked up but thanks to Sai escape and chase after Kakashi. Tsunade sends all of the K11 to stop them from getting in the way of Kakashi's sacrifice. This results in a lot of Team 7 VS the other teams, even Gaara is tasked with stoppign Naruto from proceeding, a fight he ultimately loses. Kakashi aand Naruto eventually defeat Hiruko and grow closer.
CHIKARA ARC
MAIN VILLAIN: Kabuto Yakushi
Neji, Lee, Tenten & New Team 7 get sent on a mission to 'The Hole' encounter a mid-experimental Kabuto Yakushi. This plot is basically the same as the actual anime arc itself except the little girl subplot and the K11 back-up is removed. Meanwhile, a stoic Jiraiya sets off for the Hidden Rain and fights Konan & the Animal Path, ultimately dying.
HUNT FOR ITACHI ARC
MAIN VILLAIN: Deidara, Tobi & Taka (Itachi and Kisame are ambiguous)
Because both Itachi and Kisame are on the run and their whereabouts have been spotted, this arc will be a big one as not only are Team 8 and Kakashi looking for him but so are the runaway Team 7, Tobi/Deidara, Sasuke and the rest of Taka. As Sasuke enters Suigetsu and Kisame have a friendly brawl, Kisame gives Samehada to Sui, ominously claiming he won't 'need it anymore'. Kisame dies in this arc.
A protective seal is put up and whilst Naruto, Kakashi, Sakura try to capture the Akatsuki/Hebi guys and vice versa, inside the real Uchiha fight is happening. Itachi wins but drops at the last moment, having Sasuke as the winner. Tobi then reappears but for the first time looking serious, he uses a blinding jutsu and the Akatsuki and Sasuke disappear (kamui'd but ssh we dont know what that is yet)
Naruto and the tracking ninja walk onto the battlefield and find Sasuke gone but Itachi's dead body. He's smiling. They return to the village disheartened where Naruto learns the news about Jiraiya. It's revealed via 'Tobi' (wearing a different mask) that Itachi wasn't a saint but was forced into killing his clan, he made bad decisions but meant well for his brother- and only joined the Akatsuki to spy on them and left when they started killing Jins. Sasuke changes the name to Taka (this is a pretty important arc)
NINJA HISTORY TIMELINE ARC
MAIN VILLAIN: None
This is a quieter more varied arc to pace out the big action of the last 2 fight-packed arcs. Naruto and Tsunade grieve over Jiraiya before meeting Pa Toad and going to train at Mount Myoboku. We see his training at the beginning and ending of the arc. The point of this arc is worldbuilding and to learn more about obscure ninja.
Every chapter would be a short story or day in the life of a random legendary ninja. There could be a Tobirama story, a Mangetsu story, a Hanzo story, a Sasori story, a Zabuza story...we get background info on interesting ninja we would otherwise probably not meet in a more relaxing and interesting arc. We also get the Obito and Killer Bee introductions in these timeline flashbacks. Subtly throwing in our main villain Obito and important Jin Killer Bee as the new Team Taka fight him.
PAIN INVASION ARC
Another near-perfect arc. The only change I make is that Kakashi is injured not killed and those who died stay dead, Nagato does not revive them because that's f*cking stupid and means Hinata would be remembered awesomely. There's no specific Team featured in this one. Chouji and Ino fight with Kakashi instead of Chouza- to repay them for Kakashi's help with Hidan. We finally see the scene from the prologue where Sage Mode Naruto appears.
5 KAGE SUMMIT
MAIN VILLAIN: Sasuke & Tobi
This arc is pretty much the same as well. Whilst the 5 Kage are gathering the 3 remaining members of the Akatsuki (Kakazu, Sasori & Deidara) have had their leader Pain killed and the newbie seriousTobi take control, clearly not the person they thought he was. The 3 of them feel used and stage a coup d'etat- the three of them VS Tobi. They lose and are all badly hospitalised, seeking refuge in the same town Kakazu slaughtered in his youth, defeated and disgraced.
The new Kage are introduced and explored in more depth. Danzo survives in this version and escapes the summit before Sasuke can get to him. Meanwhile Tobi declares war and Team 7 reunite with a twisted, darker Sasuke and a Taka who are getting more and more hesitant to follow Sasuke.
KONOHA LOCK-DOWN ARC
MAIN VILLAIN: Danzo and the Foundation
Danzo escapes back to Konoha where he is still the Hokage and protected by his strong previously established Root locks down the in-ruins Konoha and is ready to make the final stand against those who hunt him. (The other villages and especially Sasuke Uchiha) This is a big arc for Sai who has to gain his freedom and fight the Foundation.
Tobi kamuis Taka to the Leaf where they stealth their way in, later on into the arc Naruto and the others return to the village to see it taken over by the ANBU and the Foundation under Hokage's orders. Naruto is captured (9 tails) and our heroes find themself pitted against their elders and friends. Kakashi, Guy, Yamato, Sakura and Sai against the village's ANBU, Foundation members and High Jonin. Sasuke has his final stand with Danzo, killing both him and Karin.
NINJA WAR
MAIN VILLAIN: War Mask Tobi, Kabuto & later Madara
(also the turtle island stuff gets it own arc but that perfect so moving on)
Despite all of the hate this war arc gets I think it's pretty much perfect. The war is more bloodthirsty and more fodder kick the bucket. Edo Itachi and Nagato are more of a big deal, being a duo that holds back an entire division, they get their own battlefield. We see some of the people we met in the Timeline arc and Madara Uchiha KILLS the 5 Kage.
Kabuto loses to the Uchiha bros by coming undone emotionally. He starts getting clumsy as he gets mad and eventually summons whatever Edos he has left to the cave, only thing is- he has become so weak and insane that the control over them is weak and the angry controlled corpses turn on Kabuto- killing him. (I'm a huge Kabuto fan but I honestly think this would be a better ending for him) Sasuke meets the 4 Edo Hokage and they head to the battlefield.
Obito is unmasked to be Tobi.
FINAL ARC
MAIN VILLAIN: Obito & also Madara
The final battle is long but nowhere near as long as in our real version. The 2 enemies are Madara and Obito, but like in the real version they also struggle for power against each other. The arena is bigger than just the 1 wasteland and takes place over a few locations (like how Shikamaru and the beach division fought the Gedo Mazu but now thats at the end) Madara takes over the battlefield and looks like he'll be the final villain whilst Obito & Kakashi 1V1 in the Kamui dimension. After a few chapters of no word from them Obito appears out of the dimension holding Kakashi's corpse, taunting Naruto with it. (This is more effective than just killing off Neji randomly)
The 4 Hokage show up and get their screentime, Tobirama, Hashirama and Hiruzen fight Madara whilst Minato helps Naruto and Sasuke against the Juubi Jin Obito.
Madara is defeated and sealed, the 3 Hokage sacrifice themselves to do so. And Obito is the final villain, his defeat in the manga is absolutely perfect and due to his physical and mental decay triggered by killing Kakashi, like in the original manga NARUTO is able to defeat him physically and mentally. Obito falls to the ground and in a second Sasuke executes him, for both trying to corrupt him and for killing many Uchiha. Naruto, who had been inside Obito's mind and had saw him is angered by this and killing him wasn't the way.
This ends the war arc but also cements the strong rift between Naruto and Sasuke. In my version Sasuke has better chances of becoming Hokage, he joined Akatsuki but also killed Itachi, Obito AND (public wrong-doer) Danzo Shimura, if anything he's a rogue hero in this version to the village. Sasuke has suspicious plans for the Bijuu and is keeping Orochimaru around as his aide but also wants to become Hokage.
FINAL EPILOGUE
FINAL VILLAIN: None. Mutual fight between Naruto & Sasuke. Oro but only for an open ending.
Timeskip aaaaaaaand final fight. Naruto is waiting at the Final Valley for him, it's a very different fight to the ones we've seen before as it's more mature in tone. Naruto and Sasuke both tie and are on the verge of killing each other in one final rasengan/chidori clash but then they realise they've always been the perfect tie for each other, in every single way.
Both realising that this way can only end in both of their deaths and looking back at the cycle of hatred they've seen from those who came before them (Oro/Jiraiya, Hashi/Maddy, Elder/Younger Son) (WHICH BY THE WAY IS A FAIRY TALE IN THIS VERSION. BC THE SONS ARE A STUPID IDEA AND YOU DONT LITERALLY DO THEM KISHI UGH) and they watch over the ninja world together. Naruto as the Sun (Orange Hokage) and Sasuke as the Moon (silent protector) meaning there is always someone watching over them.
Even further time skip and Naruto has a baby boy. Orochimaru attacks Konoha with the 10 Tails and Naruto seals it within his son, believing in him that he has the power to control it one day. Except this time, he'll be with his son to guide him through it. FULL CIRCLE.
End.
Now I know it won't happen like this but this is just my individual interpretation of the perfect Naruto story and how i'd handle such a great series as this. Please don't crucify me, it was a lot of fun contemplating and creating this so please enjoy, tell me what you think.
ARC #1 - RESCUE THE KAZEKAGE
In my opinion this arc could be improved on the most, lots of potential.
You must be registered for see images
MAIN VILLAIN: Deidara & Sasori
-The show instead of starting with a Sasuke flash forward actually shows a glimpse forward to the mid-point of the series, and shows a mysterious shady figure destroying Konoha- we see an obscured Sage Naruto summoned with the boss toads. Cut to black.
[video=youtube;CyMqS99jXNQ]https://www.youtube.com/watch?v=CyMqS99jXNQ[/video]
-Back in modern day, Naruto returns to the village (with actual new jutsu and techs) after the 3 years with Jiraiya only to find out that things in Konoha are very different. The usual K11 gang have grown apart and actively avoid each other after the Sasuke incident, Shikamaru got everybody almost killed and thus there's problems between them. Naruto obviously tries to fix this but is roped into doing the bell test against Kakashi (which is a real but light-hearted fight to showcase how strong Sakura & Naruto have actually become (like Ninja Storm 2 boss fight)
You must be registered for see images
-Gaara is kidnapped by Deidara and Tsunade sends the K11 as one big unit to deal with the global affair led by Kakashi. Because of their bad teamwork they split into groups, Team 8 tracking, Team InoShikaCho VS Sasori instead of Kankuro etc.
-The villains of this arc are Sasori and Deidara. No members die in this first arc. After being defeated in their 1v1s and getting Gaara stolen back (how it happened in the OG manga) they decide to go big and take the Sand Village by seige, using both Deidara's dragon and Sasori's 100 Puppets. This traps the K11 in the Sand Village and forces them to work together thanks to Naruto's leadership. They protect each other and become allies again, showing Naruto has brought them back together- eventually Gaara awakes and finishes them, forcing them to retreat.
-At the end of the arc as they return Hidan & Kakazu appear to the defeated 2 and tell them news that Itachi Uchiha and Kisame Hoshigaki have gone rogue from the Akatsuki and need to be hunted down.
TENCHI BRIDGE ARC:
You must be registered for see images
MAIN VILLAIN: Orochimaru and the Sound Village
This arc is mostly perfect, personally I would make Sai more powerful to make him more relevant for future arcs and more mystery surrounding Orochimaru and Sasuke, even so far as to venture into the 'Sound Village'.
This arc is basically the existing one mixed with the House of Orochimaru! filler from part 1. We get to see more of The Sound Village and fight Kabuto & Oro at the bridge, Oro's experiments and Kimimaro (who is still alive cough COUGH) and finally at the end Sasuke, who Naruto, Sai & Sakura properly fight together. This fight is more like the Storm 2 fight and it ends with Oro stopping Sasuke from killing them with Kirin, stating he wants them alive.
NOTES
-Naruto should have been taken on arcs or even just short missions to meet or encounter the other Jinchuuriki. If there was one every arc or so it makes sense for Naruto to meet them and THEN for them to be captured, ominously leading to the 9 tails.
-The Tenchi Bridge arc is a Team 7 development mission but the other Teams (Team 8, Team Guy) get equal screentime, being partnered with Naruto/Team 7 on future missions, Team Asuma get good coverage in Shippuden but the same can't be said for the likes of Kiba, Neji & Lee.
HIDAN & KAKAZU ARC
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This arc is pretty much perfect already, Hidan dies, the only big change is that KAKAZU IS NOT KILLED. HE ESCAPES.
HEBI FORMATION ARC
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MAIN VILLAIN: Kimimaro and Itachi
Much like the original arc except more dramatic and a self-contained story. Sasuke has a real fight with Orochimaru and recruits the 3, all agreeing to help each other fulfill their own goals. Jugo wants to cure his disease & be controlled, Suigetsu wants to collect the swords of the Mist and Karin wants freedom and to kill the man who butchered her mother, Kimimaro Kaguya (a better goal than getting laid) whilst Sasuke's goal is to still to get revenge on Itachi.
Jugo is kept under control by Sasuke, Sui goes to Zabuza's grave and gets the sword and Karin starts (genuinely) falling for Sasuke. All whilst being followed by Kimimaro. Hebi VS Kimimaro but instead of killing Kimi, Karin decides to move on with her life and let him go, whilst still refusing to forgive him. Sasuke sees this & thinks about his own drive. Meanwhile through all of this Naruto is learning more jutsu
Sasuke slowly starts to remember the closeness of being in a group and is reminded of Team 7. He shows signs through this arc of slowly regaining his humanity, even showing slight interest in the (SWEET AND SMART AND NOT CREEPY) Karin, finally showing signs of being able to move on with his life when Deidara and Tobi appear, telling him that his brother has gone rogue, triggering Sasuke's lust again and giving him a reason to join the Akatsuki.
THE WILL OF FIRE ARC
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MAIN VILLAIN: Hiruko
This arc is the plot of Naruto movie 3. I know this seems random and kinda dumb but this film is actually fantastic and does a lot for character development, fitting in perfectly with the Naruto storyline. Kakashi hasn't been seen for a while in this version (since the Hidan&Kakazu arc) and so this arc is mainly about him and Naruto.
You must be registered for see images
The missing nin Hiruiko (old friend of the Sannin) tries to bring about the end of the world, Kakashi lets himself be controlled and goes to them to sacrifice himself for the sake of the village. Naruto and Sakura are locked up but thanks to Sai escape and chase after Kakashi. Tsunade sends all of the K11 to stop them from getting in the way of Kakashi's sacrifice. This results in a lot of Team 7 VS the other teams, even Gaara is tasked with stoppign Naruto from proceeding, a fight he ultimately loses. Kakashi aand Naruto eventually defeat Hiruko and grow closer.
CHIKARA ARC
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MAIN VILLAIN: Kabuto Yakushi
Neji, Lee, Tenten & New Team 7 get sent on a mission to 'The Hole' encounter a mid-experimental Kabuto Yakushi. This plot is basically the same as the actual anime arc itself except the little girl subplot and the K11 back-up is removed. Meanwhile, a stoic Jiraiya sets off for the Hidden Rain and fights Konan & the Animal Path, ultimately dying.
HUNT FOR ITACHI ARC
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MAIN VILLAIN: Deidara, Tobi & Taka (Itachi and Kisame are ambiguous)
Because both Itachi and Kisame are on the run and their whereabouts have been spotted, this arc will be a big one as not only are Team 8 and Kakashi looking for him but so are the runaway Team 7, Tobi/Deidara, Sasuke and the rest of Taka. As Sasuke enters Suigetsu and Kisame have a friendly brawl, Kisame gives Samehada to Sui, ominously claiming he won't 'need it anymore'. Kisame dies in this arc.
A protective seal is put up and whilst Naruto, Kakashi, Sakura try to capture the Akatsuki/Hebi guys and vice versa, inside the real Uchiha fight is happening. Itachi wins but drops at the last moment, having Sasuke as the winner. Tobi then reappears but for the first time looking serious, he uses a blinding jutsu and the Akatsuki and Sasuke disappear (kamui'd but ssh we dont know what that is yet)
Naruto and the tracking ninja walk onto the battlefield and find Sasuke gone but Itachi's dead body. He's smiling. They return to the village disheartened where Naruto learns the news about Jiraiya. It's revealed via 'Tobi' (wearing a different mask) that Itachi wasn't a saint but was forced into killing his clan, he made bad decisions but meant well for his brother- and only joined the Akatsuki to spy on them and left when they started killing Jins. Sasuke changes the name to Taka (this is a pretty important arc)
NINJA HISTORY TIMELINE ARC
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MAIN VILLAIN: None
This is a quieter more varied arc to pace out the big action of the last 2 fight-packed arcs. Naruto and Tsunade grieve over Jiraiya before meeting Pa Toad and going to train at Mount Myoboku. We see his training at the beginning and ending of the arc. The point of this arc is worldbuilding and to learn more about obscure ninja.
Every chapter would be a short story or day in the life of a random legendary ninja. There could be a Tobirama story, a Mangetsu story, a Hanzo story, a Sasori story, a Zabuza story...we get background info on interesting ninja we would otherwise probably not meet in a more relaxing and interesting arc. We also get the Obito and Killer Bee introductions in these timeline flashbacks. Subtly throwing in our main villain Obito and important Jin Killer Bee as the new Team Taka fight him.
PAIN INVASION ARC
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Another near-perfect arc. The only change I make is that Kakashi is injured not killed and those who died stay dead, Nagato does not revive them because that's f*cking stupid and means Hinata would be remembered awesomely. There's no specific Team featured in this one. Chouji and Ino fight with Kakashi instead of Chouza- to repay them for Kakashi's help with Hidan. We finally see the scene from the prologue where Sage Mode Naruto appears.
5 KAGE SUMMIT
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MAIN VILLAIN: Sasuke & Tobi
This arc is pretty much the same as well. Whilst the 5 Kage are gathering the 3 remaining members of the Akatsuki (Kakazu, Sasori & Deidara) have had their leader Pain killed and the newbie seriousTobi take control, clearly not the person they thought he was. The 3 of them feel used and stage a coup d'etat- the three of them VS Tobi. They lose and are all badly hospitalised, seeking refuge in the same town Kakazu slaughtered in his youth, defeated and disgraced.
The new Kage are introduced and explored in more depth. Danzo survives in this version and escapes the summit before Sasuke can get to him. Meanwhile Tobi declares war and Team 7 reunite with a twisted, darker Sasuke and a Taka who are getting more and more hesitant to follow Sasuke.
KONOHA LOCK-DOWN ARC
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MAIN VILLAIN: Danzo and the Foundation
Danzo escapes back to Konoha where he is still the Hokage and protected by his strong previously established Root locks down the in-ruins Konoha and is ready to make the final stand against those who hunt him. (The other villages and especially Sasuke Uchiha) This is a big arc for Sai who has to gain his freedom and fight the Foundation.
Tobi kamuis Taka to the Leaf where they stealth their way in, later on into the arc Naruto and the others return to the village to see it taken over by the ANBU and the Foundation under Hokage's orders. Naruto is captured (9 tails) and our heroes find themself pitted against their elders and friends. Kakashi, Guy, Yamato, Sakura and Sai against the village's ANBU, Foundation members and High Jonin. Sasuke has his final stand with Danzo, killing both him and Karin.
NINJA WAR
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MAIN VILLAIN: War Mask Tobi, Kabuto & later Madara
(also the turtle island stuff gets it own arc but that perfect so moving on)
Despite all of the hate this war arc gets I think it's pretty much perfect. The war is more bloodthirsty and more fodder kick the bucket. Edo Itachi and Nagato are more of a big deal, being a duo that holds back an entire division, they get their own battlefield. We see some of the people we met in the Timeline arc and Madara Uchiha KILLS the 5 Kage.
You must be registered for see images
Kabuto loses to the Uchiha bros by coming undone emotionally. He starts getting clumsy as he gets mad and eventually summons whatever Edos he has left to the cave, only thing is- he has become so weak and insane that the control over them is weak and the angry controlled corpses turn on Kabuto- killing him. (I'm a huge Kabuto fan but I honestly think this would be a better ending for him) Sasuke meets the 4 Edo Hokage and they head to the battlefield.
Obito is unmasked to be Tobi.
FINAL ARC
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MAIN VILLAIN: Obito & also Madara
The final battle is long but nowhere near as long as in our real version. The 2 enemies are Madara and Obito, but like in the real version they also struggle for power against each other. The arena is bigger than just the 1 wasteland and takes place over a few locations (like how Shikamaru and the beach division fought the Gedo Mazu but now thats at the end) Madara takes over the battlefield and looks like he'll be the final villain whilst Obito & Kakashi 1V1 in the Kamui dimension. After a few chapters of no word from them Obito appears out of the dimension holding Kakashi's corpse, taunting Naruto with it. (This is more effective than just killing off Neji randomly)
The 4 Hokage show up and get their screentime, Tobirama, Hashirama and Hiruzen fight Madara whilst Minato helps Naruto and Sasuke against the Juubi Jin Obito.
OTHER DEATHS (both on & off-screen)
-Might Guy (REAL 8 GATES and dying like a man)
-Akamaru (sacrifices self for Kiba)
-Mifune (way of the samurai ends)
-Kakazu/Deidara/Sasori (trio formation fights back too on the final battlefield)
-Sai
-Shikaku & HQ
-Cee/Darui
-Various Hyuuga members & more K11 parents
-Genma/Izumo/Kotetsu
-Kurotsuchi/Kitsuchi
Madara is defeated and sealed, the 3 Hokage sacrifice themselves to do so. And Obito is the final villain, his defeat in the manga is absolutely perfect and due to his physical and mental decay triggered by killing Kakashi, like in the original manga NARUTO is able to defeat him physically and mentally. Obito falls to the ground and in a second Sasuke executes him, for both trying to corrupt him and for killing many Uchiha. Naruto, who had been inside Obito's mind and had saw him is angered by this and killing him wasn't the way.
This ends the war arc but also cements the strong rift between Naruto and Sasuke. In my version Sasuke has better chances of becoming Hokage, he joined Akatsuki but also killed Itachi, Obito AND (public wrong-doer) Danzo Shimura, if anything he's a rogue hero in this version to the village. Sasuke has suspicious plans for the Bijuu and is keeping Orochimaru around as his aide but also wants to become Hokage.
FINAL EPILOGUE
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FINAL VILLAIN: None. Mutual fight between Naruto & Sasuke. Oro but only for an open ending.
Timeskip aaaaaaaand final fight. Naruto is waiting at the Final Valley for him, it's a very different fight to the ones we've seen before as it's more mature in tone. Naruto and Sasuke both tie and are on the verge of killing each other in one final rasengan/chidori clash but then they realise they've always been the perfect tie for each other, in every single way.
Both realising that this way can only end in both of their deaths and looking back at the cycle of hatred they've seen from those who came before them (Oro/Jiraiya, Hashi/Maddy, Elder/Younger Son) (WHICH BY THE WAY IS A FAIRY TALE IN THIS VERSION. BC THE SONS ARE A STUPID IDEA AND YOU DONT LITERALLY DO THEM KISHI UGH) and they watch over the ninja world together. Naruto as the Sun (Orange Hokage) and Sasuke as the Moon (silent protector) meaning there is always someone watching over them.
Even further time skip and Naruto has a baby boy. Orochimaru attacks Konoha with the 10 Tails and Naruto seals it within his son, believing in him that he has the power to control it one day. Except this time, he'll be with his son to guide him through it. FULL CIRCLE.
End.
Now I know it won't happen like this but this is just my individual interpretation of the perfect Naruto story and how i'd handle such a great series as this. Please don't crucify me, it was a lot of fun contemplating and creating this so please enjoy, tell me what you think.
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