Disclaimer: I don't own Naruto, if I did then Naruto would be able to fight his opponents without relying on luck and last second power ups.

Note: I'm sorry about this, but I was having a really hard time continuing the story, so I decided rather than abandoning it I would do a summary chapter to cover highlight points that I was planning on including. I would be fine with someone picking up the story message me about it and you can use the whole thing as long as you credit me. I may also pick this thing back up myself eventually. Sorry for not being able to complete it.

Summary

Naruto and company return to Konoha and report to Tsunade. Sai tests Naruto, is immediately defeated and Naruto drops him off at T&I. Tsunade still sends Tenzo and Sai with Naruto and Sakura to the Tenshi bridge mission. The main difference is that Sai is more respectful to Naruto as he has shown superior talent. The meeting at the bridge is again interrupted by Orochimaru. Tenzo and Sakura combat Kabuto and capture him while Naruto fights Orochimaru with Sai observing the battle in the background. Naruto uses the Kyuubi's chakra to keep Orochimaru on the back foot as the corrosive nature of the chakra makes it harder for Orochimaru to regenerate. As Naruto is in control of himself and a sensor Orochimaru can't retreat when he is on the back foot in the fight and unleashes his eight branches technique. This is easily countered by Naruto's chakra chains as they are perfectly suited for fighting giant monster like creatures. When that failed Orochimaru released his soul-self (the white snake thing Sasuke fought) in a last ditch effort to survive by taking over Naruto's body. Naruto was expecting it and used a scroll that he and Jiraiya prepared to seal Orochimaru's soul-self in an enclosed area. Naruto then goes on to explain that Orochimaru's immortality technique was impressive as it created a chakra construct that could hold his consciousness, but it had a fatal flaw. The issue was that the construct needed a host to stabilise itself. That meant that all Naruto had to do to kill Orochimaru was prevent him from finding another host, which is what the seal array he and Jiraiya made was meant to do. The rest of the team gather to watch as Orochimaru's soul-self disintegrates. They wake up Kabuto and force him to watch before interrogating him to find Sasuke's location. They then move to the base where Sasuke is staying after securing him with Sai's ink, Tenzo's wood and Naruto's seals and in Tenzo's direct keeping. When they reach Sasuke he taunts Kabuto about being captured before attacking Naruto with his sword. Naruto grabs his wrist to block and Sasuke congratulates him on blocking the correct way. He then enters Naruto's mindscape to suppress the Kyuubi, but is surprised to find that he can't as Naruto is the one controlling the flow of the chakra rather than the Kyuubi. Naruto tries to convince Sasuke to come back with them stating that as long as Sasuke remains by his side Itatchi will come to him because of the Kyuubi and the fact that he defeated Orochimaru. Sasuke is unconvinced until Naruto explains that Sasuke would be coming with them because he had already sealed his chakra as Sasuke let him hold his arm for to long. When Sasuke challenges the proposition because chakra sealing isn't used in combat Naruto counters that the reason is that it takes almost double the chakra you want to seal in a person in order to do so, but that isn't an issue for him as his chakra reserves are almost infinite compared to a normal ninja's. When they leave the mindscape Sasuke tries to channel chakra and finds he can't before agreeing to come with them as they have proven to not be useless. Kabuto is interrogated and then executed.

They take Sasuke to Tsunade's office and try to get Sasuke to be officially reinstated when Danzo barges in and demands that he be executed as an example. Tension is high before Naruto asks why Danzo has a sharingan. Danzo is apprehended and they find that he has Shisui's eye in his head and the senju sharingan arm. There is a bit of time when they kill root agents trying to free him, and they look over his root files. Eventually Sasuke is probationally reinstated under the same rules that Konoha has for any other missing nin. Which means that he was given a seal kill switch that can be activated by the Hokage or their minder which in this case was Naruto. Danzo was unofficially found guilty of treason, but officially charged with bloodline theft and Sasuke is allowed to execute him as he had stolen Sharingan. As part of his reinstatement Sasuke then guides Naruto's team through the bases that Orochimaru had. They pick up Karin and Suigetsu individually and take them back to Konoha, then when they are on the way back from the base that held Jugo they are ambushed by Itachi, Kisame and Tobi. Naruto notices Zetsu, but can't do anything as he is forced to fight Kisame solo while Sasuke fights Itachi and Tobi distracts the rest of the group. Sasuke's fight with Itachi is like cannon except the eight branches technique is never used. When Naruto fights Kisame he finds that Samehada doesn't absorb nature chakra, and decides that's because if it did then it would kill its wielder or turn to stone itself. Naruto and Kisame have a huge slugfest, but Naruto eventually wins and Samehada takes a liking to his chakra and becomes his sword. After the other two fights are over Zetsu notifies Tobi and he disappears kidnapping Sasuke and taking Itachi's eyes. Naruto feels it happen and the team return how with Jugo in tow. Tobi tries to turn Sasuke against Konoha for revenge, but Sasuke states he can't as the still has the kill switch. In addition to that Sasuke argues that Danzo is completely to blame as he held one of Shisui's eyes which is capable of Kotoamatsukami which has the ability of mind control, and he had already had his revenge on him. In a fit of rage Tobi kills Sasuke.

Later there was a sighting of Kakazu and Hidan in fire country and Naruto's group is sent out to deal with them. During training before the fight Naruto learns how to seal using only his chakra. He also trains Karin in the use of chakra chains. The fight with Kakazu is a bit more one-sided than in cannon, but generally the same. Hidan on the other hand is fairy easily demolished and Naruto seals what is left into immobility (his head, torso and limbs separate). Naruto then realizes that this isn't the real Hidan it is actually a seal and blood based clone. The blood base makes it seem real and the seals make it an immortal clone. The group then follow the chakra thread attached to the Hidan clone back to where it comes from. On the way there Zetsu strays to close and Naruto manages to eject him from the ground there is a fight, but without his ability to hide Zetsu is reasonably easily dealt with. When he dies Tobi immediately shows up. Naruto stabs him with a chakra chain and Tobi laughs at his saying he will need to do much better to hurt him. Naruto replies that from the observations of the previous fight he never changes his momentum or teleported while he was phasing through anything. So Naruto would only have to wait out his technique and/or chakra in order to win the fight. He is right and Tobi's voice changes ranting at them at how he was Madara Uchiha, how he was immortal, how he killed Sasuke and how he ran the Akatsuki from the shadows. When the time on his technique runs out there is a spatter of blood as he's impaled, but he uses the Izanagi to change reality so that the injury never happened. Tobi then goes on at how he only had four spares left after everything in the Kamui dimension was destroyed in a massive explosion and how he would never forgive Kakashi for that. There is a huge fight, but it ends when Naruto impales him again and again waits out the time necessary. During the fight Naruto figures out how he needs to fight with Samehada, which was by using it as a shield for jutsu rather than as a weapon. They then find the Jashinist temple where Hidan's real body is in stasis while his spirit inhabits his clone. They then execute Hidan and destroy the temple before returning to Konoha.

Later Jiraiya comes to Konoha and states he found out who is running the Akatsuki, the Amekage. He then takes Naruto with him to confront him. During the training Naruto did after defeating Tobi with Samehada he became a facsimile of a true sage by running sage chakra through Samehada enough that it became able to absorb it for him. They confront Pein and Konan outside of Ame. Jiraiya manages to defeat Konan while Naruto was holding of the six paths of Pein and then together they defeat Pein reasonably easily. However, Naruto was forced to use a combination of the Kyuubi's chakra and nature chakra to complete the feat. They confront Nagato directly and along with the prowess they showed him and the fact that Tobi had been defeated he is convinced to follow their path to peace and allies Ame officially with Konoha. In the following years there are a couple more scuffles, but eventually all the nations are allied. It started when the new Mizukage joined the Suna-Konoha-Ame alliance and then after some fights that were put up in protest the Raikage and Tsuchikage followed suit. Eventually when Nagato dies from the demands of the six paths technique as well as the rinnegan Naruto is gifted the eyes. By this point Naruto had completely mastered sage mode and the Kyuubi's chakra, but he can't do a full transformation as the Kyuubi hates him. He however is able to use all of it's chakra as his own is strong enough to overpower it. After Naruto spends years mastering the rinnegan he uses a combination of the eyes, yin-yang release, Orochimaru's immortality technique and Hidan's clone technique to create a body of pure chakra for himself and places his soul inside of it. This has the side effect of destroying his body and freeing the Kyuubi, but rendered him as immortal as a bijuu. He did so that even after he would have normally died he could combat the Kyuubi and stop it from destroying whatever it wanted. He and the Kyuubi then spent the rest of eternity in endless combat.

Note: Well that's the summary, not sure if the ending of the story is that satisfying even if I had written it out longhand. Though this does have the ideas I had for exploits or ideas in Naruto. If you have questions feel free to ask them, I'll try to reply.