The AO3 version has two embedded pictures, if you want to check them out. They're why the actual chapter is so short. Also, there's a poll on my profile about what you want to see next. Drop by!
The Organization is older than heroes. If heroes and villains are the two loud siblings whose fighting takes up the family's attention, then the Organization is the unobtrusive cousin no one in the family really knows, and so awkwardly ignore. This is not a new state of affairs. The Organization has been around ever since governments the world over started using Quirked individuals to give themselves an edge, then took advantage of the treaties that outlawed Quirk warfare to establish itself as the foremost authority on Quirked Asset Management and the premium provider of Quirk using mercenaries.
Surprisingly, its success was not due to ruthlessness or underhanded measures. Well, not its own, at any rate. At a time when Quirked individuals were seen as oddities and assets at best, tools and lab rats at worst, the Organization distinguished itself through treating its employees with integrity, and dealing with potential threats in good faith. While the world met Quirks with wariness and scorn, and the individuals in government employ were often unexpectedly eliminated, possessors of useful, blatant, or too-dangerous-to-live abilities were offered stable employment of the grayer sort in the Organization. After all, if all the world played Bad Cop, why not be the good one? Therefore, it was only expected that such people flocked to the Organization's banner.
And the foresight of the Organization bore fruit. Mercenaries were willing to accept reduced rates in exchange for surety of non-betrayal, leading to competitive prices. Security and safety at home base meant greater effort spent on training, increasing agent quality, which, combined with the decision not to eliminate out of paranoia, in turn led to reduced turnover rate, resulting in more experienced operatives, and consequently far more optimal performance and mission outcomes,
The Organization built itself a reputation. It offered high quality at (relatively) low prices, discretion, and a distinct lack of fanaticism.
Even as the tides of public opinion turned and the Hero system was midwifed to confront the everyday evils of villainy, the players in the game of nations found their hands tied when dealing with the gray complexities of interests, alliances, trust, and betrayal, for it had become diplomatically damaging to be seen to employ Quirks directly, and shadowed facilities had long since turned into boogeymen that few would come near, let alone be trained in for black-ops. Not to mention, one could hardly ask heroes, the brave defenders of justice, to lie and spy and kill. Other pieces would have to be found. And so, the Organization was put in the ideal position to gather blackmail, thus ensuring that not only could it protect its own, it was itself protected from destruction as it took on its current form:
A motley assembly of gods, half out of myth, workers of miracles. Removed from petty mortal bickering, but not unwilling to act when conditions were met; yet willing to be kind, and finding strength in kindness; still battling against true evil, despite its claims of amorality.
And so, by the time Orochimaru grew again into his own, there was an excellent Konoha-substitute for him and his partner to gather their strength and learn the dance of politics and war.