It all began when Tsunade accepted the Amegakure ninja's plea for medical assistance. Though, to be precise, that might not even be the real beginning. Perhaps the true cause dates back even further—perhaps to when Jiraiya, as Konoha's own, assisted the Akatsuki in sealing the Tailed Beasts. From that point, one could trace the chain of events that ultimately led here. A few lines can describe it all.
From Tsunade's perspective, it went like this:
If Jiraiya hadn't lost Naruto, he wouldn't have known the Akatsuki's true aim in collecting the Tailed Beasts. Without that knowledge, he wouldn't have known of the Otsutsuki clan. Without knowing that, he wouldn't have helped seal the Tailed Beasts. Without helping seal them, he wouldn't have encountered a non-human named Kita. If he knew nothing of Kita, he wouldn't care about her survival; if he didn't care, Tsunade would not have risked so much to heal a non-human.
If she hadn't treated Kita, she might have died—but what did that have to do with Konoha?
Alas, life isn't hypothetical, and the chain goes deeper.
If Tsunade hadn't treated her, Danzo wouldn't have exploited the incident. Without Danzo's manipulation, the non-human affair would not have caused a scandal. If there had been no scandal, the Daimyo wouldn't have reprimanded Tsunade. Without that, she wouldn't have lost the Daimyo's trust and eventually the Hokage position, replaced by Danzo.
In short: Jiraiya, in his "generosity," had handed Konoha's assets over to the Akatsuki, and Tsunade, in a rare show of conscience, had agreed to treat a non-human.
Going even further:
If Jiraiya hadn't delivered the Nine-Tails, if Naruto hadn't lost control, he wouldn't have become the prime target of the village's upper echelon. Then Sasuke wouldn't have had to support interrogations, nor would he have betrayed Sakura at a critical moment, which ultimately triggered Konoha's Non-Human Uprising. Without the uprising, Danzo would not have used the situation to implicate Tsunade.
And what caused all this?
If Kita hadn't wandered the streets of Konoha, unseen by the vengeful Ibiki, none of this would have happened. Or looking further back, if Kita had simply submitted to Ibiki at the time, he would have had no reason to retaliate. Indeed, the Land of Fire forbids non-humans from standing, but Kita could have lived normally if Ibiki had turned a blind eye. Therefore, the Non-Human Uprising was Kita's fault.
And Kita's fault gave Danzo an opportunity.
Without Danzo's schemes, Tsunade herself would have played her hand poorly—but if Danzo didn't exploit it, he wouldn't be Danzo.
When Tsunade's authority was shaken, he mobilized the clans, visiting every influential household. The final tree standing? The Hyuga.
And then the Byakugan came to him.
Had Tsunade been ruthless and expelled the boy with the Byakugan, people might have called the Fifth Hokage cold and heartless. They might have murmured for a while, then forgotten. But now, Tsunade had become the Sixth Hokage.
Years ago, had Hizashi Hyuga not sacrificed himself for the clan's head, Hiashi would not have felt guilt, would not have sought to compensate his brother's orphan, and would not have seen the faint cyan glow of the Byakugan's pure potential.
If Sharin had not stubbornly clung to the Hyuga, Hiashi would never have confirmed that this cyan Byakugan could evolve further.
Those outside our clan must think differently. What does it have to do with Konoha?
Everyone has selfish desires. Danzo did. Hiashi did too. He betrayed for his debt to Neji. He obtained the Byakugan, freeing Hyuga Neji's "caged bird." He felt at peace—and if given the chance again, he would act the same.
Hinata, too, acted on personal desire. Her love for Naruto, though unrelated to all the chaos, was selfish. Without it, she would not have pretended to comply with Sharin, avoiding an arranged marriage for herself and Neji.
Neji had desire as well. Without it, he would not have fought to gain Hinata's acceptance of his Byakugan.
As for Sakura's defection, the Haruno couple's suicides… in the midst of upheaval, these were minor events.
Everything started with a non-human. Had Kita not absorbed Black Zetsu and gained its full memory, none of this would have happened.
She was gone from Konoha, yet she had thrown the village into chaos.
"It's like this, Nagato," Obito said, glancing at the silent Itachi. "I won't lie—I'm pissed if you attack Konoha. But if you do, I won't stop you. Sharin… I can't just let that go. He's naive, yes, but how can we ignore it? People aren't supposed to do that. Where's their conscience? How can anyone endure having their eyes taken? Those eight locking needles—who could endure that?!"
Obito could not bear it. Neither could Nagato.
"No matter how dark or contradictory Konoha is, I am Uchiha Itachi of Konoha," Itachi said, looking at Nagato with clear, unsullied eyes. "Thank you, Pain. You let me know all this, trusting me to decide. She may not be blood, but he called me brother. I will not ignore him. In this matter, it's the Hyuga clan—I would slaughter them all if vengeance were necessary."
His stance was resolute, not perfunctory. Nagato did not doubt him; Itachi's strength needed no lies.
Yet one problem remained: hatred.
Killing does not resolve hatred. When Nagato spoke again, it was with measured gravity.
"Obito, Itachi… when I was a child, my parents were accidentally killed by Konoha ninjas during the Second World War."
This was a secret known only to Konan and Kita, not even Obito. Itachi was surprised; Obito was astonished. Nagato waved off any questions.
"Listen. They weren't ninja—they were Konoha soldiers returning from battle, scavenging. I made a sound. They thought I was the enemy and killed my parents. Seeing I was just a child, they realized the mistake. Ridiculous—they patted my head and said sorry. That was my first taste of hatred."
He sat on the empty hospital bed, looking through the window at the endless rain.
"This was my first real pain, caused by Konoha. The second, Yahiko's death. The third, Konoha and Hanzo together. I was blinded by hatred, killing all linked to Hanzo. If not for Konan stopping me… Konoha never left a good impression. Sharin's case adds another layer. I promise you, Obito, I do not move against Konoha in your lifetime—not out of compulsion, but because I am trying to resolve the cycles of hatred. If I had attacked Konoha to punish those who harmed Sharin, the survivors would hate me. Itachi, your choice to annihilate your clan also recognized this truth, didn't it?"
He smiled faintly, as if detached, like a wild crane floating among clouds.
"What do we do then? Sharin's fate is just… let go?!"
Obito fumed. Back then, Sharin and Kita had smiled brightly, like the full moon in the sky. Now? His heart was frozen, seeing the living harm of those who had sacrificed everything—for a pair of eyes, for meaningless power struggles.
Nagato shook his head.
"This resentment… I can't swallow either. But hatred continues. Seeing that crack in the world helped me understand: the world isn't bad—it's people who make it so. Obsession over irreversible matters changes nothing. Hatred can make people strong, Obito, but also destroys them. Your powers could topple Konoha, but it would be useless. They took Sharin's eyes? Then let them lose too. Only by sharing the same pain can people understand one another. No need to annihilate the Hyuga, no need to destroy Konoha. Destroying solves nothing. The Hyuga's unwillingness to give Sharin their eyes? Then leave them be."
As Nagato said, wiping out the Hyuga would solve little. It would relieve temporary anger but change nothing. He had been impulsive.
Itachi, half-comprehending, asked, "Did you destroy the Byakugan?"
Nagato nodded.
"Killing doesn't solve problems. Only tasting darkness allows one to hope for light. Experiencing war's pain allows hope for peace. Itachi, I won't speak further of you—look back at the peace we've enforced… is it truly worth it?"
Itachi did not know whether his past was right, nor if he should regret it now. He did not dwell, instead looking to Nagato and asking again,
"What of Sakura's parents' suicide—"
"What?!!"
A sudden voice at the door startled them. It was Sakura, not eavesdropping, but coming to inform Nagato of Sharin's situation. Yet in this empty ward, she overheard a staggering revelation.
"Itachi, what did you say?!"
Sakura was shocked, stepping forward to grab Itachi's shoulder. "Suicide? Who? What happened?!"
Her grip hurt Itachi, and his expression showed annoyance, though it was due to her sudden arrival. He barely freed himself and stepped back, saying nothing, not even looking at her face.
In truth, he had known all along: Sakura's defection would inevitably affect her parents. Previously, nothing had happened because of the Fifth Hokage. Now, under the Sixth, the outcome was predictable—they had committed suicide, perhaps to avoid implicating Sakura.
"Calm down, Sakura!"
Obito said firmly, trying to ground her amid chaos. But it was almost impossible. She took a step back, dazed, muttering,
"No… no… my parents can't be dead! Sensei is still here! Sasuke promised to help Sensei! No… and Kakashi-sensei… no! Absolutely not!"
Then, she spun around and bolted outside.
"Sakura!" Obito shouted, moving to stop her—but Nagato blocked him.
"Let it be, Obito. I'll go." He sighed slightly and stood from the bed. "This is the only chance to tell her about her parents."
"You did this on purpose? Chose this moment?" Itachi asked incredulously.
Nagato nodded.
"Where else could I tell her? When she left Konoha, she was already abandoned by everyone."