Nominally Ninja

It's widely admitted that Zetsu is, in fact, a complete problem in all corners of the Naruto universe. Some are in the camp that he's to be considered one of Kaguya's sons, others her will made manifest in its entirety. What we can say for sure is that Zetsu caused problems and they were far-reaching. The plant tried to influence things and cause discord everywhere it went for a thousand years, sometimes more successfully than others. The Zetsu we first meet in the series is sort of a final form kind of Zetsu. It's latched onto a slightly idiotic hive mind that it didn't initially have access to, though how quickly it managed to make up for this after the first time the tree was cut off from being able to trap people in dreamlands is impossible to say.

It's very likely it happened relatively quickly.

All the same, one thing that Zetsu seemed to have figured out quickly was that Hagoromo's children were easier to get at than Hamura's. In my personal timelines, this is because Hamura's daughters fucked off into the wind to do their own thing rather than settling into being proper noble ladies. Meanwhile. Asura and Indra were right there. To their misfortune.

Zetsu didn't work obviously at first, clearly. No, in the beginning, he was just a whisper in the wind, a word in someone's ear and a hint that had someone singing Asura's praises over Indra's when Asura never went looking for praise in the first place. It was someone suggesting tests when the test itself was a trick. It was someone who leaned into Hagoromo's darker, more inhuman tendencies and pointing out all the ways that that was ideal. Hamura probably saw the edges of it, the way the lean was going, but what could he do? He had his own catastrophes to deal with and he knew his own failings where their mother had been concerned. It was why he willingly ceded the empire to his brother, after all. It's very likely he didn't realize what it was doing to Hagoromo's children.

Hagoromo, as we know, picked his younger son over his elder. What is never clear is why he didn't make it clear that the boys were in competition. The implication of disappointment is strong, and Indra's expediency was scorned. Asura, dawdling about to teach, yes, but also to take his sweet time doing what he liked, wasn't exactly picking the right path for a solid leadership of an empire. Being beloved is never wrong, but doing it at the cost of everything else in your lands but a small fraction is never wise. We never get to see what else Indra did. We only ever get to see the handful of instances that Hagoromo didn't approve of. We only know that Zetsu seized on the rift their father drove between the brothers and made himself at home.

We don't see, immediately, why he picked Indra for this. Indra had the eyes, certainly, but Asura was the one weak to being taken advantage of. Perhaps it was because, ultimately, Indra was brittle while Asura would bend and bend even if it wasn't to his benefit. Regardless, Zetsu handled both the brothers differently, and this carried down their family lines, down the transmigrations from generation to generation. And at some point, Zetsu got less subtle.

Everyone knows that Zetsu messed with the Uchiha. They look at Indra, Madara, Obito, even Sasuke and go 'See? That's the family he was messing with.' They forget that the Zetsu army was fueled by Hashirama cells. They forget that Yamato vanished for most of the war because he'd become a prisoner and that at the end of the initial story we really had no idea if he'd survived. Mokuton came from the tree that Kaguya ate the fruit of, most likely, and Zetsu needed it because it was something he couldn't replicate on his own. It could give him things nothing else could, and lend strength to his minions in a way that he likely had waited a very long time for.

The Senju he took a light hand with, but the hand was there. At first, it was whispering to drive the brothers apart, yes. But later, it was other things, fanning on the exuberance of Asura's line and encouraging it in murmurs on the wind, pressing for a more hotheaded nature that sharply rejected thinking ahead, that didn't take the time to listen. And this is where it started to get tricky. With emotion came volume. They were yellers, they were singers, they were many things that were vibrant, bright, and wildly alive.

Because this suited Zetsu, and kept the tensions between the families sharp, after a few generations he started to actively take a hand. When there was a quiet child that went exploring, he'd pick them off. It was a simple enough thing, at the times he chose, and at first, it was a rarity, a sometimes. It was a child who left the safety of the group. It was the child who was curious. It was the child that observed and paid attention to things that others didn't notice. It was any child he'd determined was a sensor, or one he'd noticed might realize something was off. And over time, those numbers grew. As the battles between Senju and Uchiha heightened, he found ways to get the Uchiha blamed for the deaths of the more exuberant children, and took out the quiet ones, fueling rumors inside the clan that everyone just knew that quiet children were at risk. That there was something wrong with them. That they were fey and liable to be taken back by nature itself before ever seeing maturity. And these things meant that people tried not to get as attached to the quiet ones, to pay as close of attention to them so that when they vanished in the night on a wander it wouldn't hurt as badly.

This didn't always work, of course. Tobirama is a wonderful example of this as Hashirama clung to him in his younger years, and given Hashirama had Mokuton as well, it was a risk Zetsu simply wasn't able to take. He got him eventually, later on down the line after the village was formed.

The Senju, after all, were a founding clan of Konoha, they were a large group, they were equal to the Uchiha in numbers. And yet, somehow, they all vanished until it was just Tsunade. Some theorize that they married into civilian clans and were absorbed, and I can agree that at least some had this happen. But what of the rest? What happened to all the shinobi? Where did the many clans go?

For the Senju, it circled back to that intensity of emotion. They threw themselves in battles in the first war, and that lost both the first and second Hokage. They threw themselves into the second battle and that lost Nawaki and his entire genin team in one fell fall. But nothing is said about the Senju off-screen. How many Senju went on missions that were just that touch harder than the information said they should have been? How many Senju went out and just never came back? This probably contributed to the depth of Tsunade's grief if not only her close family, but the entirety of her extended one, seemed to slowly vanish over the course of her lifetime until one day she looked around and realized she was the only one left.

Zetsu had what he needed from Hashirama, by then, and could turn all of his focus to the Uchiha since the Senju had been neutralized.

Once Zetsu folded Indra enough that he had a foothold, there was no way he was ever going to let go. He pressed on the tender spots that followed his fall from Hagoromo's grace, fanned the flames of anger in his children, and slowly, carefully, steered them into habits that would lead to quiet resentment, reading into things that other people don't notice, and nonverbal communication that most outside the clan had little hope of understanding.

He carefully, meticulously, tweaked verbal accounts about how the Sharingan worked any time there seemed to be a misstep in the family doing it properly, and over the generations picked out things that had been written and preserved by previous generations and simply... rid them from the family library. Once, Indra's love of knowledge, his libraries, were vast. There was fuuinjutsu, to say nothing of the many other jutsu created or discovered over the generations that various Uchiha had written down for their children. It was, after all, something that the clan did, recording things for the future, for those that came after to learn and build upon. Zetsu slowly, carefully, got rid of those things that would threaten him. By the time of Konoha, the Uchiha had nothing of sealing but storage scrolls, and thousands of techniques had been snatched from the library, to say nothing of most of the theory. The stone about their eyes as well... tweaked and changed and wrong in the most misleading of ways.

Of course, this wasn't all Zetsu did. He was never content to simply passively doing things, and as he found some success in manipulating the way of the Senju, so did he start to steer the Uchiha more blatantly. At first, his approach was quiet, a creeping in the night where a particularly fussy baby, one who cried in a way that said they were aware, was turned over in their basket to quietly suffocate in the night. He was careful to start with the loud ones, the ones that were annoying and active and liable to turn in their sleep. But, as he always did, this didn't linger at just that. He started to make the loud children vanish when they'd run off to play, only to turn up savaged like they were caught by an animal. He started to carefully pick off first children who slept alone, quietly suffocating them when they finally dozed off in the night. He found a way to take care of the quiet ones that worried him and get the Senju blamed until they were actually involved.

The actions were noticed, of course they were noticed, but the stories that sprang up around them were different than those among the Senju. Instead of distancing themselves from children to be lost the Uchiha learned to cling. Between stories of their eyes and the way that deaths happened, the Uchiha turned to pairing off their children, a tradition of giving care from older to younger, to having their children either in the room with a new parent or with their older children always, even with the fussy babies. Fussy babies became a cause for fear and worry because a fussy baby would attract the notice of a night creeper and would have their soul devoured in the night. They learned to hush their youngest until they were strong enough that a creeper wouldn't get them, and stealth became a vital skill in the clan as their ways got more intense, quieter and more focused.

Zetsu wasn't well pleased by the way the Uchiha banded together, but he still used it, picking out an Uchiha or several in each generation to influence and follow, until finally, he found Madara. Had he chosen someone else, things might have gone differently, but Madara was strong, inventive, and terribly desperate for the world to become a good place. He was everything that Zetsu had been looking for, and was the same age as the Mokuton user that had sprung up in the Senju clan. Thus, he had Madara's older brothers dealt with so that he had more room to work, ripping the boy's protection away without any hesitation. It bound him tighter to his younger brother, and he let it rest, for a time, leaving Izuna's babies, fussy, alone for once, letting the exhaustion wear on the young man until he fell in battle and left Madara vulnerable to his whispers in the most powerful way.

And he moved. He wrapped Madara around his fingers and ripped him from the safety of his clan, going after the ties that kept the Uchiha protectorates safe because they posed their own threats to him and he wouldn't abide them. For a time, that was enough. The Uchiha were protected inside the village with the police, they took a blow when Madara left and the whispers that Zetsu started against them were all too easy, but they settled, the Uchiha proving themselves with their loyalties and ties to one another and the village as a whole.

So over time, Zetsu started to go after those Uchiha who left the village. It was subtle, at first, and they were beacons scattered across the nation int he way their chakra baseline was usually the same steady thrum that synchronized when thrummed. They were understandable losses, and he didn't take all of them, leaving those who were exceptional alone. One day, he acquired Obito and finally knew he had his opportunity by how the boy survived that he'd been able to fall through solid stone and come out the other side, if not whole, then alive. He brought him to Madara, then pressed and prodded to make sure he sent the boy off in the right direction. He ensured that everything was just so.

Once all that was settled neatly enough, he poked and prodded and made a test of his control by sending the boy to Konoha, in getting the Uchiha in an untenable position with the most protected of the bijuu. Yes, he couldn't claim it then, that had never been an option, but that wasn't why it had been released. Instead, it was a careful ploy to deal with the Uchiha. The rumors that followed were from his plants, at first, before they caught on and gathered steam. Any time they made headway he whispered in someone's ear to tighten their restrictions, to hem their effectiveness, to cut off their ability to get money until the entire clan was penned and had nowhere to turn. In this, Hiruzen's refusal to see what was in front of him was a boon and was likely why Hiruzen's successors seemed to be so thin on the ground. If someone died because they were dishonored, such as Hatake Sakumo, for instance, then all the better to keep someone in control that Zetsu could use to further his agendas.

Of course the Uchiha didn't handle being penned in well. They weren't designed for that. They thrived on new experiences and stretching their boundaries and they'd been forced into ever smaller roles for generations. Of course the Uchiha wanted to fight back. They had no recourses left. Zetsu had to do nothing at all, at that point, and simply watched as the Uchiha fell, only taking care to locate everyone on the resonance that he'd been tracking them through for so long and dealing with them before they knew they weren't safe. Thus the Uchiha fell until there was a negligible number, which he knew would only shrink, and thus be no threat at all so he could leave them be.

That thinking hardly went well for him, as we all know, but it almost did. It so very nearly did.