Naruto returns to the village after so many years away he's now 16 years old he's wearing his Shippudden outfit with a black chunin vest that has orange stripes he has a white sash with orange kanji on it over the years while Naruto has been gone Anko and Sasuke have had their curse marks removed everyone has improved over the years by alot Naruto walks through the front gates suprising Izumo and Kotetsu as they never expected him to come back here he never signs in and they don't make him as they don't think that he will be staying once he finds out what's changed since he's been gone .
Naruto sees a memorial for the Ichiraku family as they have been murdered his blood is boiling he continues on keeping his face neutral every viilager sees his face and starts throwing stuff at him threatening to kill him if he doesn't leave he continues on he reaches the hokage's office instead of walking right inside he sees Danzo as Hokage right away his instincts are screaming at him to find Tsunade he vanishes before he can be seen but one of Danzo's root saw him and she sighs at his return hoping that he doesn't find out about Tsunade's fate or those that chose to stand with her.
It takes Naruto no time to find the records of what happned to Tsunade her Shizune Anko Hana Kurenai Tsume Rock Lee Yugao Ino Tenten Shikamaru Shino Choji Genma Raido Ibiki Jiraiya Iruka were senteced to be sold as sex slaves for the women and regular slaves for the men luckily it hasn't happened yet nor has their chakra networks been severed just sealed for now but each person is in a medically induced coma so that they can be transported Naruto sends clones to transport each person to mount Myoboku right away as Jiraiya gave him a map to it and how to get past the maze there they successfully make it there without any problems except the journey and gathering everything required depleted the clones of their chakra.
The toads try to free everyone from their slumber under the orders and guidence of the last clone but they lacked the power who wouldn't dispell once everything was done properly on Tsunade he dispelled once he gets the memories back Naruto now has no problems getting his revenge or letting everyone know that he's back but not yet first he needs to prepare the battle field he heads to the forest of Death and sets traps all over the entire forest as well as every training ground he sends clones to every one of them he even leaves one here then lowers his chakra signature lower than a civilian's then heads to the bridage in wave to watch the show.
Each clone begins flaring it's chakra there's even one in the arena that they use for the chunin exams Danzo as well as everyone else feels this humongus surge of chakra and thinks right away that it's the 9 tails coming back for Tsunade he smirks until he finds out after looking at the monitor that she and all of her supportors have been taken he growls then sends his root after him sadly all of them except Fu Torune Sai and Yakumo die Danzo heads to the one in the arena thinkijng that he will be safer there he's wrong Danzo looks him over he doesn't notice anything that impressive excpet his sash other than that nothing impresses him about the 9 tails.
Naruto's clone says you can't fool me Danzo and none of your fancy ideals are going to save you from my wrath the only reason I've spared your life up until now is because of Hiruzen just before he died he left me a letter begging me to not to kill you and I've honored his request also if you wanted to be hokage so badly all you had to do was ask Tsunade she never wanted to come back here Danzo is shocked as she said that exact thing to him that the only reason she accepted it was to protect the person standing in front of him Naruto says if I had chosen to never come back here you would have been hokage years ago Danzo sighs then asks if all of this is true why did those that sided with her fight so hard against me Naruto says because of how you run things in Root lets face it you suck at it.
Danzo scowls then asks what do you mean Naruto says use me as an example you wanted me as a weapon correct Danzo nods Naruto says instead of corecion kidnapping brainwashing or murder you could try idk seduction manipulation subterfuge but all you care about is what you want and your own power that ends now Danzo tries to use the Kotoamatsukami on Naruto but he just deflects it back at Danzo who falls for it as he can only use that sharingan once per day so naruto tells him to die and that's what danzo does he chops off the arm with the sharingans in it and kills himself Naruto takes that arm back to Tsunade at Mount Myoboku once he gets there Tsunade jumps on him wrpas her arms and legs around his body and kisses him he is shocked but doesn't fighr her he kisses back once she stops kissing him.
He sees that she isn't back to 100% yet and that's why she's the only one awake Naruto takes a scroll he takes her away from all of them then takes some of her chakra adds it to the scroll he makes hers take it over and then he adds all of the chakra in the scroll go to her which is 1 tails worth of chakra and more than she's ever had coursing through her body in her entire life he also uses some of it to heal her the rest of the way and make sure that her henge is no lomger neccesary that what she looks like is what she's going to look like for the rest of her life as he also activated her Uzumaki genes once that's done he shows her the arm she gasps in shock he takes the cells from the arm adds it to hers and gives her wood style along with Hashirama's healing factor but she will never be able to use his sage mode.
Tsuande implants two sharingan in Naruto's eyes she also makes sure that he keeps his original eye color and that he can turn them off instead of being like Kakashi but he will never have Mongekyo just regular 3 tomoe Sharingan Naruto seals the arm away then they wake the others he does the same thing to them that he did to Tsunade except for Hashirama's cells they all feel better and stronger than ever Naruto tells them that this increase in power will only last 1 year unless you train it to merge with your chakra network they all nod in understanding then immediately start training in how to control their new chakra they do every chakra control exercise there is Jiraiya redoes the Rasengan training as his final one but Naruto has them all do shpe manipulation and also has them train in their elements.
Once they finish doing so the chakra merges with their chakra networks Tsunade is shocked to discover that she can use wood style Naruto heads back to the village he sneaks into her compound steals ever wood style jutsu he does the same with the hokage vault then comes back he gives Tsunade every justsu he could find she smiles at him then frowns as he stole from her compound and from the hokage vault she is mad at him until he tells her everything that Danzo did to her she growls saying that I actually thought he was going to protect the village once I stepped down I even almost signed the documents for him to have full control over everything except my family and your family's things he didn't like that which is how I'm guessing we ended up almost sold to our enemies.
Naruto says that's not even the worst of it the village is under a massive genjutsu right now everyone believes that Danzo is their god I have the chakra to break it but not the knowledge to break a genjutsu of that scale Kurenai says I can but I lack the power to do it Naruto takes her to the village she senses the genjutsu sighs then says this is beyond my skills in genjutsu even with Naruto closes his eyes focuses his chakra over the genjutsu he smirks then pulls out an empty scroll he draws everything that he saw then explains it to Kurenai he says it's not that difficult to dispel as you're making it out to be not beliveing him he shows her the scroll she is shocked that it's so simple that they merely put up a chakra dome to loop feed and conatin the jutsu over the village so that Danzo could o whatever he wanted and everyone would be his blind little drones.
Naruto says only problem is that he tied his jutsu with the one over our village that protects us and the one that we use to sense enemies Kurenai sighs Naruto summons a toad then sends a copy of what he found out to Tsunade 15 minutes later he gets a reply back saying do it he and Kurnai nreak the jutsu then Naruto sends clones to break everyone out of their stupefied state once that's done Naruto uses the last of his chakra to restore the two barriers however he changed the way that these two functioned instead of the protection one being active all of the time he sets it up so that the barrier corps needs to activate it when the village is being attacked and the sensory one is always active.
Afrer all of the barriers have been fixed Naruto uses Kyuubi's chakra to fill his reserves then sends clones to check the defenses of the village sadly after a clone pops in each fortiification they have fallen into disrepair so Naruto has his clones tear them down and rebuild them from scratch he also puts seals on them to keep them in perfect shape normally such a job would have taken almost 5 years to complete but with Naruto's clones it only took 5 hours after that is done he sends every one to the hospital gets them checked out brings back everyone he saved to a complely fixed village except for the civilians and shinobi are out of comission Tsunade heads to the hospital after checking them over even if she had unlimited chakra they still won't recover back to how they once were in no less than 6 months.
the civiklans however she can have them up and running in 1 month so that's what she focuses on first as they provide income for the village once that is finished she works on Hinata Sakura Hana just getting those girls back into shape plus teaching the other two how to be medics which is what Shizune is doing it takes awhile as the 3 that she is focsing on already have mednin training she was going to train Ino and Tenten as well before she got sidetracked by Danzo and Hana she just increaed her skills as a medic to include humans also to include more animals than just dogs in fact a year before Danzo made his move Tsunade put Hana through a bunch of training and rigours testing to become an officially recognized vet of Fire Country.
She became certified in over a dozen species she even got her certificate for wild animals not just domesticated pets while all of this is going on Naruto is using his clones to go to every department the village has and fix everything that Danzo broke he also undoes every law that made Danzo a living god and them have no rights other than to breathe he also puts everything back to the way it was right before he left instead of it looking like a empire he restores the village back to how it used to look before he left he also destroys the genjutsu on the hokage monument instead of every face being Danzo's it now shows the four past hokage's along with Tsunade's face added to the mountain.
After they are back up and running again thanks to Naruto lending Tsunade and her students purified Kyuubi chakra they were able to heal everyone and put them back to how they were before Danzo meddled with them sadly their abilities were cut in half but they were fine with that it just meant that they had training to do which is what they do they train alongside Naruto until they become 4 times stronger than they were before right after getting some rest they get word that Gaara has been captured by Akatsuki Naruto alongside Kakashi Sakura.
Team Gai is sent along as backup they first reach the Suna grab Temari on the way then heal Kankuro while that is happening Chiyo agrees to go with them Sakura stays behind to heal Kankuro Temari goes in her place the head to the land of Rivers they catch the trail of the Akatsuki and come across a five point barrier team gai handles the tags but they produce copies of each of the ones who remove them makeing it difficult to fight but each member of Team Gai actually likes the challenge the only two who switch opponents are Neji and Lee as they know that they can easily beat their own duplicates but switching makes it harder.
Naruto breaks down the boulder as they are trying to seal Shukaku away next he launches a fireball at them making them jump away next he throws explosive tahs at the statue making them stop the sealing and save the statue as they just started they were expecting Kisame and Itachi to stall them with transformed clones but they didn't have time to set it up Pain looks at Naruto he looks at the jutsu they were using then scoffs and says let me guess you were using the 9 phantom dragons jutsu every Akatsuki member twitches in shock wondering how he could possibly know that.
Naruto laughs then says you idiots have no idea what you are messing with if any of you gets one hand seal wrong or misjudges the amount of chakra needed to perform the jutsu it won't work on your intended target it will work on you all as a whole instead and there will be no stopping it until it has consumed you all body and soul Deidera looks at Pain then says you never told us that Pain says that's because it's only a myth it's as old as the biju themselves so I felt no need to share it with you all.
Naruto says actually it's not a myth there's a reason why the shinobi of the sky don't exist anymore and it's not because they were wiped out by any nation they used the exact same jutsu to try to conquer the zero tails but wound up being aborbed by it instead as the beast used it's power to turn the jutsu against them and absorbed everything that they were each year it tricks some fool into learning the jutsu and absorbing them into itself for knowledge and power what it's really searching for is the perfect vessel to merge with one that won't be tricked into falling under it's spell just like you all have been.
Pain growls then says I am a god no creature can command me to do anything Naruto asks then why are you all taking orders from Zetsu and being puppets on it's string I mean it makes no difference to me I'll gladly kill all of you if you continue with this path before anything else can be said Sasori attacks Naruto who only frowns and dodges every attack he makes some clones then attacks using jutsu of every element Deidera tried to help but he was killed by a Chidori from Kakashi after the death of the two Akatsuki members Gaara was taken back to the village other than chakra exhaustion he was fine with that they went back to the leaf village but Kakashi knows that right away Naruto needs more attacks in his arsenal so he decides to contact Jiraiya who agrees to train Naruto he takes him to the forest of Death puts him through rigerous survival training then has him do every chakra control exercise there is including shape manipulation.
Once done he has him learn the rasengan with his clones he gets it mastered in a week next he gets trained in wind manipulation he does every exercise in fact he does them for every element as before he just learned the jutsu next he learns how to combine the wind element with his rasengan he uses clones enough to do the elements of wind lightning and fire it takes him a month but he is able to make Rasenshurikens of the three elements but so far he can't seem to throw them yet he keeps practicing until jiraiya says you're trying to hard instead of just trying to maintain the jutsu all of the time just create it then try to throw it then let it do what it needs to do after it leaves your hands Naruto nods after some practice he's able to throw them but sadly he can't combine them yet it's much too dangerous even with clones.
Until the Kyuubi gives him an idea but before he can try it an anbu shows up requesting his presence he arrives in front of Tsunade she says I hate to disturb your training but you're needed on an urgent mission Team 10 is requesting backup and you're the only person available Naruto nods then leaves to go after them he gathers all of his gear including his sword then rushes to where Team 10 is currently fighting Hidan and Kakazu right before Hidan's weapon is about to make Asuma bleed it's met with Naruto's sword and deflected back at him making himself bleed.
Naruto quickly sees that choji and Ino aren't here Asuma looks at Naruto with surprise then with anger that he was the one sent as he thinks that it's his fault that they were on this mission in the first place seeing Asuma's anger Naruto back hands Asuma sending him flying making the others quirk an eyebrow along with Akatsuki he picks Asuma up by the thraot looks him dead in the eyes then says I can't believe someone as weak as you was one of the Guardian Shinobi 12 I almost feel disgusted to be considered one of your bretheren you're a disgrace to the sash that you wear.
If you don't shape up and begin training again village or no village I will kill you with that he tosses Asuma like a rag doll making the others flinch he turns to the Akatsuki members bows to them then says I'm sorry that you had to fight such a weakling now we can fight for real and show these upstarts why ninja were the things to be afraid of and everytime it was uttered by samurai they pissed themselves in fear that they would be next Hidan si shivering in fear and excitement at the killing intent that Naruto is letting off Kakazu however is unnerved by the sheer pressure of it.
Naruto rushes them and begins trading blows to see what they are capable of he jumps back creates several clones grabs the other out of the way then creates his wind style rasenshuriken then trows it at them they bare have time to defend themselves before he creates a lightning one as well as a fire one and kills both of them Naruto is impressed at the devastation he then turns to the shocked members of Asuma's team as well as the others that made up the whole mission Naruto says whatever your mission is you can complete it now or you can come back to the village with me.
Asuma says we will complete our mission as we only have a few things left to do Naruto nods then leaves back to the village he reports back to Tsunade all in all his mission took 4 days to complete he tells her everything that happened she scolds him about using his new jutsus and labels them forbidden she says if he uses the combined one again she will strip him of his ninja license and his rank he just shrugs she scowls then lets him leave she gives him a month long break with orders to do no training at all he nods.