How to build a flexible and scalable system for PCs' NPC organizations?

Question

Background:
I am preparing to run a campaign using Dark Heresy Second Edition. Although this is nominally an investigative game, several key non-combat mechanical systems are either anemic or missing outright - which makes sense when you consider its lineage coming from table top wargaming.

I want my Player's Characters to build, maintain, and grow their own organizations similar to Eisenhorn. There is effectively zero mechanical support for this in the system currently, although a few elements are there. To solve this issue, I intend to build (hopefully not from scratch!) a system that can effectively model these organizations. It is this enterprise (building said system) that brings me to RPG.SE for assistance.

Question: How to build a flexible and scalable system for PCs' NPC organizations?
From my research to date, there is no single, self-contained, ruleset from any RPG system that meets all of my needs.

1. If there is one that would be suitable for porting to DH2, please point me in the right direction.
2. Otherwise, I need help in cobbling a system together, either from scratch or by merging existing mechanical systems.

Amplifying information follows:

A bit more about the organizations:
In the early game, PCs will be building their organization manually, one NPC (or so) at a time. As they grow in power and Influence, so will their organizations. I can envision the organization members recruited early on becoming part of the PCs' personal retinue or inner circle. Eventually they will run their own sub-organizations as the PCs' lieutenants.

These organizations will eventually become large and multifaceted. For example, a PC could eventually have an estate, an intelligence network, cults for false flag operations, criminal organizations, legitimate businesses to raise funds and act as fronts for covert operations, groups of researchers, libraries of occult and forbidden texts, etc. Each one of these sub-organizations would be run by one of the PC's agents (generically referring to any NPC working for the PC) and may or may not be aware of each other. Each one would be staffed with yet more agents.

I want these organizations to be developed in play. I would also create NPC-operated organizations that could be friend or foe, and then these various organizations (PC and NPC both) interacting with one another.

What I want to avoid:

• Excessive abstraction

Many of the systems I've encountered that do something like this are very abstract. They often give the organization attributes similar to individual characters, but are otherwise 'hollow'. That is, they don't contain actual characters that actually do things - all of this is abstracted away into the various attributes.

I am definitely NOT trying to ask how to populate an organization with NPCs, but I do want a system that mechanically reflects the individual NPCs (i.e. it doesn't just abstract them away, and leave me to paint them in afterwards).

• Scaling difficulties

The most often recommended systems that model organizations seem to scale well in isolation (you could model anything from a small family to a galaxy-spanning empire) but fall apart when interacting with other organizations at different scale levels.

I am looking to find/make a system has scale-flexibility baked in. From one perspective (CS), these organizations are recursive. From another (Set theory) they are proper sub-sets. They need to be able to interact with one another on the same level, and from different levels (upwards and downwards).

• Setting specificity

With a few (really one) exception, all of the extant systems I've looked at are deeply predicated on the setting. This usually comes in the form of medieval political power structures with houses or noble families, and geographically-defined domains or realms. While my immediate goal is to use this in DH2, I want to be able to take this system with my table to whatever systems we play in the future.

My research so far:
I've been thinking about this for about two months now. I started here at RPG SE and found many great leads. Here are some related Questions I've found:
Contacts, and how to use them?
How do I teach my players to (covertly) gather intelligence?
Any mechanics out there for developing and maintaining a spy/information network?
How to build an organisation in pathfinder?

As a result, I have purchased several books and been reading up on the relevant systems:

• Reign Enchiridion
• Adventurer Conqueror King
• Houses of the Blooded
• SWN
• Houses of Hermes: Societies (Ars Magica)
• And a few others that I'm currently blanking on. (I will update this list once I get home)

I've also asked basically the same question on the FFG forum. While I got a few good ideas, I did not receive a full answer addressing all of my concerns and goals.

Answer 1

There are two questions here, but they seem to be a bit blended. Let me address them in turn.

How do can I let PCs run an organization in a way where their actions and mechanical ability matters?

The best system I've seen for this is the Second Edition Exalted 'Creation-Ruling Mandate' system, as described in their source Masters of Jade. In this system, the organization as a whole does have stats, measuring it's population, the competence of the average member at what they do, how far the organization can reach and wield their power, how influential the organization, and the material wealth the organization possesses. Also tracked is the Policy of the organization, how it regularly behaves and the share beliefs among the employees, if it has any sub-organization/partner/parent organizations, or if it has some special resource that defies any of the previous general categories. There are then the mechanics of the type of actions leaders can take to grow their organization, protect what they have, or attack other organizations.

It's well built, mechanically sound, and works to have PCs in the seats of power in trade empires and nations... and yes on the surface this does seem like a dry and empty frame work, much like the systems you've found, I expect.

This is where the second question comes in:

How do I make organizations the PCs are leading/opposing/interacting with not seem like dry empty frame works?

This is a DM skills question. Given the exact same rules and dungeon one DM might say that you find; A 20' by 30' room to the left of you, with three orcs in it. Mutual non-surprise, roll initiative.

Where in another might say; The sound of your dwarven make plate echoes lightly from the walls of the roughly hewn cavern... ahead on your left is a doorway, the door broken and rotten in the hall. Inside three greenskins hurriedly finish donning their armor and drawing their swords. Perhaps you may consider lighter elven chain in the future, but now is the time of battle.

Notice how different the same mechanical occurrence was described by different DMs. It's the same with organizations. You could choose to keep them dry and empty husks, or you could populate the place with NPCs that the PC will care about. Give them a sharp tongued no nonsense bookkeeper, a one-armed munitions engineer how keeps adding 'random gene-stealer checks' to every process, from checking out a weapon to filing a complaint about gene-stealer checks. These guys don't have to be fully stated characters or have too in depth of backstories to start with, just know what their job relevant skills should be for their rank and keep good notes as they develop.

If the PCs can't populate a break room with NPCs that work for them and they want to have a conversation a few months into the campaign, then it's not going to be the organization system's fault.