Ever since his crisis Dix decided to lead a mostly balanced life. He was too intent on getting the Flying Thunder God Technique, which almost broke him inside. He understood that by focusing on one thing for so long made him lose his linear growth he had ever since he woke up in this life. For his new training schedule he decided to continue with every single projects he had before, namely Squad A-X, also he set up another similarly sized squad to train FTGT.
There was one peculiar thing that he noticed during training. His chakra became a bit different ever since he evolved his sharingans. During the fusion his chakra became more dense, thus it was possible to hold even more in his reserves. Also it became much purer, meaning less chakra was enough to do the same tasks as before. It seems like the same way Dix's blood and chakra had a huge impact on the sharingans, they had the same amount of impact on his body. Probably this could be called the prelude of gaining the rinnegans, or just a natural process that will lead to that same end. Those eyes have incredible power, by both techniques and raw stats they give.
For quite a while nothing notable happened. Dix was attending class as usual and helped Hinata train almost every day. After the first time his father just rarely showed up to see some results. She was growing at a good pace. Dix also kept up his rivalry with Kiba. He was growing rapidly because there was someone he was able to compare himself to. This usually isn't really good, but for Kiba his competitiveness is the best motivation.
Sometimes he accompanied Shikamaru to laze around somewhere and watch the clouds slowly moving on the sky. Usually Dix, after some silence, would introduce Shikamaru to concepts that were highly debated in his previous life. Scientific, moral, philosophic, technical. Sometimes he would be dismissed with a few words, while at other times Shikamaru would sit up and focus on him intently to solve a difficult problem. It was a matter of interest. If Dix managed to find something that interested him he would go really far in a debate, using every single point of IQ he had.
Months passed this way. Everyone was living their lives as usual. Soon the end of the school year came and everyone graduated from 2nd year successfully. It was around at that time when Dix felt his new eyes will fill up soon. He had to make a few preparations to evolve it, because last time his crisis carried him over the hurdle, but this time he had to do it manually.
Also, even though there were 4 chakra-transformation seals around his eyes, he only used 3 of them ever since he woke up from the last surgery to speed up the process. The fourth will be used to overclock the eyes to push them over the edge. It was already summer break when he felt like his eyes hit their limit, so he made sure his friends know he won't be available for a day or two. Hinata was a bit worried for him, but he just dismissed her worries and promised her that he will be alright.
The next morning he rushed out to his camp in the woods, greeted Yami and changed the clone taking care of her. It was like changing your dog's water in their bowl when it gets dirty. This was required of him to properly take care of her, and Dix quite liked the wolf, that was actually really large by now. He wanted to try and ride on her back, but actually she was still quite slow compared to Dix, so it would've been simply a useless thing to do. Too bad.
With his responsibilities done for, he walked out of the camp and moved to the clearing nearby where he destroyed the tree with his previous eyes. There he sat down in his own meditative position and started working on evolving his sharingans. It was a painful process. When his eyes filled up before, he stopped the flow altogether. Now he forcibly tried to get more Uchiha-chakra into his eyes, and that hurt pretty badly.
When he felt the torturing pain in his eyes to be almost unbearable he switched on the last seal to empower the eyes even more. It hurt like all hell. He was quite worried at that point that his eyes will simply pop out or burst due to the overflow of chakra. He had his eyes closed by instinct for a while now, so he tried to open them to see where he is in the process. After many minutes of incredible suffering he was about to give up when his eyesight began to fade. He was on the verge of fainting, which he actually gladly accepted. It would let him continue the process while not having to suffer more. So he let the seals open then in a few seconds he dropped on the ground.
He was drifting in the darkness. He was in his subconscious once again, and at parts he did not like to be in. Once again he was back in his own personal hell, but this time it was a bit different. In a few seconds a burning sensation washed trough his whole body, and the nightmares were swept away by an orange-red burning chakra. It decimated the worst parts, while gently washing over him. Dix woke up with a smile on his face.
When he regained consciousness he couldn't help but say out loud:
"Thanks, Kurama. You really are a life saver."
Another wave of warm chakra moved trough his body, then retreated to where it came from. It was like Kurama saying he can handle the rest on his own.
Dix tried to open his eyes, but just like last time he was blind. He summoned a clone to confirm the evolution is in progress. Dix was quite worried at what will happen. Whatever he did with the sharingans was all based on luck. All of his ideas and plans were nothing but taking chances and hoping the world works the way he envisioned it.
The basic idea was that he makes two separate Mangekyo Sharingans, and when the second one is finished he will change it out with the first one. This way a MS was switched out by another, which is theoretically needed for this to work. He wanted to try and trick the system by cultivating both eyes himself, thus bypassing the requirement that the second sharingan must be a relative's.
For now he was glad the evolution itself started. He had his doubts and worries about this, but it worked, so he was able to move on to the next step.
Actually, all he had to do was wait. The clone had to keep watching his eyes to see if anything changes. His eyes were still hurting pretty bad, but he just put up with it. After many minutes of silent suffering the clone gasped and quickly informed him that the eyes settled, and the pattern was a bit lame but was certainly a Mangekyo Sharingan.
"Okay, I suppose we just have to proceed with the original plan and transplant the first set of eyes... Wait, what?" the clone said, then noticed something quite peculiar. He shouted the last words, which scared Dix a bit.
"What is it?" he asked, then his eyes suddenly felt like they actually burst this time. He instinctively closed his eyelids due to the pain. The clone was about to shout at him, but Dix interrupted him by holding up his hand and saying.
"Yeah, I know I know, just stay shut, my head hurts enough as it is." he put a lot of effort into opening his eyes and keeping them that way. He could feel two small trails of blood leave his eye sockets.
"This is unprecedented! The eyes already settled once, but now they move again! How is this possible?" said the clone and summoned a few more of himself to join the brainstorming.
"Maybe its broken?" came the first idea right away as one of the clones was summoned. Dix frowned and clicked his tongues, but he couldn't deny the possibility.
"Maybe its having a hard time to stay stable due to the two different chakras present in the body?"
"Maybe its evolving once again, right after the previous one?"
"Maybe it failed fusing for the first time and is forced to try it again by the overflow of chakra?"
"Maybe it didn't actually finish evolving in the first place..."
"Let's just wait and see what happens..."
Many ideas came up and everyone was worried that the sharingans are broken or something similar. After a few minutes of waiting, suddenly Dix was hit with another wave of pain and was knocked out right away. The clones disappeared and Dix was left lying on the ground.
He woke up standing on a white plain. It seemed to be of marble and everywhere he looked was the same white nothingness. The air was breathable and the sky was kind of blueish. Dix couldn't see anything notable, and was unsure of his location. He started walking, then running, then screaming for help. He was lost and was scared. He was alone. But suddenly he saw the horizon split, and an orange-red Sun came up to shower him in light and warmth.
He was smiling into the sun, he would've even praised it, but suddenly his legs failed him and he fell on his back.
He expected to land on marble and hit his head pretty bad, but actually he landed on mostly soft ground, probably grass. He opened his eyes once again to see the Sun that saved him from his loneliness, at least for the last time, but he instead saw nothing. This time he had a bit more control over his body and thoughts, so he sat up and summoned a clone to see whats going on. The report came that they are back in reality, so its all right now... but there were other news.
"The eyes!" screamed the clone. Dix had no idea whats going on so he feared the worst. Even Yami heard the scream and rushed to see what happened, as a second ago the clone with him disappeared, and by now she kinda knew what that means.
"Take a look, quick!" the clone said, then summoned a few more in his place then cancelled his own. Dix was able to see trough the clone's memories that his eyes settled once again, and showed a completely different emblem this time. It was really fancy and looked equally similar to both of his last eyes.
"Marvelous! The Sharingan evolved twice at the same time! It looks like a real Eternal Mangekyo Sharingan now! And we even have spare eyes. Great! All seems to be working well."
It really was marvelous. Seems like Asura's reincarnation and the Uzumaki's blood is really something. The clones started to theorize how this could happen, and quite a few good ideas came up. At the end they agreed on the concept that the previous sharingan recorded itself in Dix's blood and chakra when they fused. The new pair used this environment to immediately proceed with the EMS evolution after the simple MS was finished.
After a few hours of recuperating Dix once again could see well, even better than before. He jumped up and told his clones:
"Okay, I'm ready! Let's take this for a test ride."
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I'll post both the 2nd Mangekyo Sharingan and the Eternal Mangekyo Sharingan on discord.
You find the official discord for the novel here: https://discord.gg/XCEDp7H9tA
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Cheers! :D