Games with espionage(infiltration/spying/sabotage) mechanics

Fallout 4, the Institute questline.

https://store.steampowered.com/app/716640/Sigma_Theory_Global_Cold_War/

Just seconding what rurnhani posted before.
It´s about the only game I can think of that fits your bill as I understand it!

Alpha Centauri had, if my memory serves, spies that were not only good, but downright overpowered.

Hearts of Iron 4 added a pretty involved espionage system with the La Résistance expansion.

Another game that would probably fit the bill is Republic: The Revolution. I don't think it's outright called espionage in that game (been a few years since I last played it though), but sending out operatives to gather intelligence is a pretty important part of that game.

The Nilfgaard faction in GWENT relies on espionage to disrupt the enemy. The player places some of their cards in the opponent's board instead of their own, letting the spies do their own thing.

Covert Action?

As the topic already been bumped, just a reminder for some folks who are like me.
You can bookmark topics by clicking the little bookmark icon right from the title.

I forgot/missed this and it got me pretty curious about these games, better save it for later ^^

edit: Imperium Galactica 2 also had a spy system with options like: sabotage building, production(?) or ship, incite revolt, steal technology, hunt down spy (offensive and defensive) and I think regicide as well.

I want to mention the War Table in "Dragon Age Inquisition" but that "direct outcome" you want doesn't really make it qualify
you have 3 advisors (Commander of the military forces of the Inquisition / Ambassador and chief diplomat of the Inquisition / Spymaster of the Inquisition) and each has their "forces/agents"
the operations on the war table, those that are essential to progress the story will always have the same outcome (no chance to fail)
the other operations could fail or succeed but they only give rewards, like gear items or resources .. there is also influence you get from those operations that you need to make upgrades related to the war table (like shorten the time it takes for your advisors forces to finish the operations, get increased rewards ..etc)

Even Mass Effect Andromeda has a meta game "Strike Teams" but you don't actually see those npcs .. it is something done from a console (you hire teams and send them to missions) but that only give small rewards (coins, gear items, stuff like that) .. they could fail or succeed.

Assassin's creed brotherhood has a mini game where you send your assassins out in realtime and I believe they continue this later in the series

Another one for the list
https://store.steampowered.com/app/1741640/Shadows_of_Forbidden_Gods/

Infiltration is a measure of how much the player has spread their influence in the World.

Most Locations in the game can be Infiltrated by any Agent by completing a simple Challenge. The agent makes progress each turn equal to their Intrigue stat. The complexity, the progress needed to succeed, is 50 plus 25 per level of Security in the location.

Almost all Locations that can be Infiltrated have 1 Point Of Interest (POI) that Agents need to Infiltrate to provide full Infiltration. City Locations have multiple POIs, all of which need to be Infiltrated to gain full Infiltration at the Location. Cities always have a "City Palace" POI that requires all other POIs to be infiltrated first.

Infiltration boosts the passive spread of Shadow to the location from neighbors with higher shadow, and infiltration unlocks other Challenges for Agents to complete.

Effect of infiltration in different locations:

Coven of witches: Unlocks the enshadow challenge (bring location shadow to 100%) and dark worship (adding shadow divided between the closest human settlements that are not at 100% shadow, and adding menace to the coven).
Orcs: Subjugated orc locations unlock the challenges expand horde (create a new infiltrated orc camp in a neighboring empty location with habitability at least 5%) and organize horde (increases orc industry in this location by 50% and in all neighbors by 25%) and the challenge retreat to the hills.
All human locations: 100% infiltration unlocks the silent assassination challenge (allowing you to kill a ruler with a lot less profile and slightly less menace than a brutal assassination) and access vault (allowing you to take or give items or gold to/from the locations ruler).
Home of any hero: Any infiltration allows the challenge poison (next time the hero rests they are disrupted for 5 turns and weakend for 25) and at least 50% infiltration allows steal (give or take any gold or items to or from the hero)
Cities: Infiltrating a city to at least 50% increases the effectiveness/speed of laying low by 1 tier. Infiltrating a city to 100% unlocks the enshadow challenge (bring location shadow to 100%) and the political gridlock challenge (city ends its current local action and instead does "political gridlock" for 10 turns, if the city is a capital the same effect will also happen to the national action).
    Docks: Unlocks the Malign Catch challenge (creates passive madness and shadow gain).
    Vast Sewers: Unlocks the start plague challenge, and allows agents to recruit vermin.
    Market: Unlocks a challenge to force the market to change the items on sale.
Holy site: Unlocks the Desecrate Holy Site challenge if shadow is at least 66% (creating passive shadow gain and preventing consecration and allowing a challenge to give you power at the cost of giving the location menace).
Farming Communities and Fortresses currently have no special effect from being infiltrated

in 7 kingdoms your spies could infiltrate enemy towns, structures to sow dissent or convert others(the npc is then controlled by the computer as if their own, but the agent works for you also) and even take over eg. enemy fort when you control the commander post.

since this topic is on live again, and since I have close to 1000 hours in seven kingdoms 1 & 2 combined.I need to add seven kingdoms 2 also here as you can play a 4 hour session map with starting focusing on getting spies from INN, and moving them to enemy, stealing their technology, causing them to create war on others and what I really love.... if you have a spy with extremely high leadership and bribed all others in fort where king is also present...

ıf you assassinate king, there is a chance that the enemy can make your spy as the king!!!!

The joy of all the things they have in the map turn into your colour, and enemy having no idea what they have done is amazing.