What Happens When You Assume
My suggestion is based on 2 assumptions:
Though you list movies as influences, I assume you want your game to resemble a TV drama like The Americans or House of Cards because of the serial nature of most RPGs. It seems unlikely to me that you would invest this heavily in a single-evening game.
You want to incorporate your players' plans and ideas - there is not a single "true" meaning behind intelligence data, nor is there a single "right" response that the players must discover and enact in order to succeed.
A Volatile Alchemy
Based on those assumptions, I'm going to suggest a marriage of 2 games (hey, you said you were up for hacking).
Hillfolk / DramaSystem
For the TV-drama aspects of your game, where convincing each other and management to follow your lead is of primary importance, I cannot over-recommend the DramaSystem, found in Kickstarter-darling Hillfolk.
In the main book, you will find the DramaSystem, an RPG system focused on creating relationship-driven, TV-series-style games. The book takes its name from the first setting designed for the game, Iron-age raiding tribes in the Levant. But also in the main book you will find 30 (yes, thirty) other "series pitches" or settings for use with the game. Most important for your purposes may be Kenneth Hite's contribution, Moscow Station, set in the CIA station spying on Moscow in the late '70s.
The system is all about interpersonal drama - who gets what they want, who gives in now to get something later, etc.. It includes a deliberately simple system for resolving "procedural" attempts - what you call "boots on the ground." Helpfully, also in the main book, you will find some small advice for grafting DramaSystem into another system more directed towards the action side of things.
Which brings us to the second game in this mixture.
Night's Black Agents / Gumshoe
The Gumshoe system (same designer - Robin D. Laws, same publisher - Pelgrane) is aimed squarely at investigative play. The core assumption is that finding clues is never what the game is about - doing something with those clues is where the interesting play lies. It was designed, I think, for the horror game Esoterrorists, and used probably most famously in Trail of Cthulhu. But it goes far beyond horror, and luckily for you, has an amazing implementation for espionage...with a side of horror.
Night's Black Agents is Ken Hite's spies-vs-vampires game and it's amazing. The game is designed to support modular play and among the dials you can set is the mood (are you Bond / Bourne types or more like Smiley?) and the degree of supernatural elements. So turn the emotional grind up (Burn and Dust and possibly Mirror modes) and the supernatural all the way down, and you've got a good start on your game.
The book provides a ton of information on spying, spy organizations, terminology, equipment, techniques, etc.. It also provides a useful framework for building a conspiracy for your PCs to throw themselves against - but it expects them to be competent secret agents, so your use will necessarily vary.
Shake (not stir) Well and Serve
Between these two games, you'll have an tool chest overflowing with sharp and specialized implements for creating the game it sounds to me like you have in mind. It's also possible that just one or the other of them will deliver everything you want. I would run this with Hillfolk alone, but that's just me.
With a twist
If you need a little more spice, I would also recommend taking a look at Jonathan Wick's A Wilderness of Mirrors at least for its fantastic planning mechanics in the genre of espionage gaming.
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Disclosure - I have run Hillfolk, but only gotten to read Night's Black Agents. I do have experience running investigative games before GUMSHOE and understand the problems that the system solves.