Everything was going according to plan. There was a standard protocol between the shinobi. When in a foreign land on a mission, they would try to spend as little time there as possible. So that was what exactly Naruto did.
He took the mission with Itachi and Shisui. They reached Suna in the morning and immediately headed back toward fire country. At their speed, they would pass the border at night. The mission was a simple scroll exchange. Naruto gave them the storage scroll with all the seals, and after a count and an inspection, they were on their way.
They were traveling lightly. Sealing their personal stuff so they could go at faster speeds. His guess was correct. Before reaching the border and with enough space not to get accidentally discovered by patrols, they got attacked.
Naruto only felt it a split second before but pushed Shisui and Itachi away as vines sprung from the ground. Naruto barely dodged away, but his arm got a shallow wound. He immediately got battle ready and unsealed a sword and a dagger.
He was going to fight with the sword and use the dagger for defense. They heard a deep voice growling. "YOU WILL NOT ESCAPE THIS TIME UZUMAKI."
Naruto expected Obito to bring back up, but Zetsu was not the one he expected. Naruto needed to lose but survive. He knew what he was doing, and Kurama was up to it. Itachi and Shisui were busy holding back Zetsu. They were using their weapons and small katons to hold off the vines.
Obito had a sword this time, and Naruto started fighting him. It was evident that Obito was trying to keep him close so he couldn't use ninjutsu and his sword to his advantage. Just like what Naruto wanted him to believe, he thought that he could only use that attack in ranged fights.
They clashed swords, and Naruto kept on defense. He was going a bit slow to play the part of exhaustion from lengthy travel. Naruto acted like he was trying to create distance, but he was failing. Suddenly a vine sprung from the ground right where Naruto was standing a moment ago.
Naruto jumped back and got closer to where Shisui and Itachi were fighting. Obito was nowhere to be found. Naruto tried sensing his chakra but couldn't find him. He must be entirely in the Kamui dimension.
Naruto went on to help others. Itachi and Shisui were fighting next to each other. Covering each other's backs. Naruto charged toward Zetsu's body. He knew Black Zetsu could not be killed yet, but White Zaetsu was different. There were replacements, but unless he brought them here, which Naruto couldn't feel, he had to go back to get another one.
Naruto slashed his arm, cutting it off, but the white Zetsu used his ability and regenerated almost immediately. He kept at it, using different jutsu and moves to destroy it, but it was hard. Suddenly he felt it.
Obito was emerging right behind Itachi and Shisui. Naruto used all his speed and threw them out of the way just as a sword pierced his chest. He coughed blood. Only standing upright due to the sword holding him.
Naruto heard his friends scream. "Pathetic. And to think that I wanted to consider you a worthy opponent. This is our goodbye Uzumaki Naruto. May this be a lesson to anyone who dares to oppose me," he said with his deep voice before leaving with Zetsu in a Kamui.
It all went according to his plan. As soon as Obito was gone, Shisui and Itachi were next to him, blood dripping down their eyes. They unlocked the mangekyou sharingan. Naruto immediately got to work. He was expecting this attack. Naruto started using a combination of powers given to him by the sage and Kurama to lessen the bleeding.
"I'm ok, guys. I know you will rightfully be mad at me, but I expected this attack to happen, so Tsunade-sama helped me prepare. She moved my vital organs away. So the blade didn't pierce my heart. There is still damage, but I should be fine in a day. We need a safe place to rest. I will explain everything." Naruto said.
Itachi and Shisui were hesitant. But when they saw the bleeding visibly slow down, and the wound started shrinking, they quickly got to work. Itachi wrapped Naruto's injury, and Shisui put him on his back to carry. They crossed the border at top speed and found a cave to rest.
Naruto fell asleep at some point, and when he woke up, it was a few hours later. He explained everything to them. How he believed that if the Akatsuki thought him dead, they would not go after Konoha. That by letting everyone believe his death, he had more freedom to take on discreet missions.
Of course, there would be limits since he couldn't wander around the village without henge, but he could stay in his shrine, which he mostly did anyway.
Naruto profusely apologized for putting Itachi and Shisui in that situation. He told them that he needed their reaction to be believable to someone who also had sharingan and could detect lies. So that was why he put them in that situation.
He apologized over and over. He knew that what he did would have lasting effects on his friends. That it was unfair. He knew it would take a lot of time for him to truly make it up to them, but he was going to do his all.
Itachi and Shisui tried to tell him that they were upset, but they understood, but Naruto didn't want them to be understanding. He wanted them to be selfish.
They were finally back in the village. It was a headache to give the mission report. Minato was not happy, to say the least. He gave Naruto an earful. But after seeing how the three boys needed some rest, he let them go.
Naruto went to the ROOT base. There were things to do. Danzo was utilizing him more and more to the point that he felt confined to the base. There were so many new responsibilities, and even by using his clones, he felt stretched.
Time passed in a blink of an eye. Naruto was 12 now. It was a few months from Genin's graduation, and Naruto wasn't really able to see many of his friends. All his friends were shining in their fields. They were as strong as they were when they were chunin, but they had more variety in their skills.
Naruto was happy to see the systems implemented in the village were fruitful, and they were getting the desired outcomes. Itachi was also going to take over soon. His father was looking forward to his retirement.
Thinking about Itachi and Shisui brought another pain to his chest. The boys were always too kind. They forgave Naruto after that incident and even went to Tsunade-hime about eye deterioration. Tsunade did an extensive search after getting approval from Fugaku.
She found out that, indeed, only the implant would stop the total deterioration, but there were things they weren't aware of before. The eyes couldn't be swapped, but the people who donated the eyes and the receivers didn't have to be direct relatives. They only needed blood and DNA compatibility.
So Fugaku gave Tsunade access to a part of their shrine. All normal sharingans were burned after death. But mangekyou were sealed and kept. Naruto suspected the ones Danzo had were probably from Uchiha, whose bodies were not retrieved, or bastards no one knew of.
After more studies, Tsunade finally managed to find matches for most of the current members who had the mangekyou. Some refused surgery since they were not active shinobi or didn't use their sharingan much in the fight.
Fugaku was also one of them. He didn't use his mangekyou to the extent that no one even knew he had it. Itachi and Shisui went for the surgery, as for a few other members. All of the surgeries were successful, and their previous eyes were given back for safekeeping in case there was a need for them in the future.
All of this was, of course, done in secret to the extent that only the Hokage, Tsunade, and the Uchiha clan were aware. The only reason Naruto knew was because Itachi and Shisui told them about it.
Something that was really bothering Naruto was Danzo. He had been acting strange lately, and his latest order was just out of character for him. he was becoming paranoid. Being harsher with agents and giving them more complex and more demanding missions.
Naruto was trying to figure things out, but so far, he had no clue what was wrong. Even he was under suspicion. But to a much less degree. As soon as Itachi became a Hokage, he would take over the ROOT, so Danzo still trusted him, but at the same time, he kept asking Naruto to prove his loyalty.
Naruto was out on a mission with Itachi and Shisui. The trio knew that these were probably their last missions. Once Itachi was the Hokage, Shisui planned on taking over as ANBU commander. His promotion was a little away, he was still learning skills to run the ANBU, but he would take it soon after.
Naruto would take his seat as the leader of the ROOT. Minato and the three sannin will be the advisors. Since Jiraiya was not always in the village, he would only take the role when he was. It was a good and robust system.
Minato planned on taking some missions to avoid getting rusty with the ANBU, but he was going to join the sealing division. He could finally spend his time researching to his heart's content. Naruto was excited for his father.
Their current mission was straightforward. They were after a group of bandits. They had quite a few rouge shinobi with them, and they've been terrorizing small cities. The group was quite large, and with around 15 shinobi of mostly chunin rank and time sensitivity, this was an A-rank mission.
They were sitting around a small campfire in a cave. It was still early to sleep. They would reach Konoha by nightfall tomorrow. A lot of attacks happen in such situations. The shinobi were pushing to get back faster, then the enemy would ambush them, and since they were tired, they wouldn't be able to defend themselves.
So this protocol has been implemented for a while that if the shinobi coming back from a mission didn't have an emergency, they would take their time. It saved so many lives with the current situations going on.
Ame decided to declare Pein publicly as their leader. After some shows of power to make it known that they were able to defend themselves, they started recruiting rogues and training them.
Everyone knew that soon there might be a war. Taki tried attacking Ame, but the whole army they sent was executed by Pein single-handedly. All but one who was sent back to tell the tale and deliver a message.
If anyone was to try attacking Ame again, Ame would declare war against them and kill them all. Afterward, other nations became reserved. They were all trying to handle their remaining rogues and prevent them from joining Ame.
Akautski was also gaining more power. They were almost done filling their ranks again, and while the new members were strong, they were also famous and well-known, so it was easier to handle them.
Naruto knew that it would be time for the next stage of his plans soon, and he was more than ready for things to finally move. Because now he was sure that his friends were prepared to overcome any and all obstacles in their way.
Never again would Naruto let there be so many pointless deaths.