Let me be clear and honest up front: Palladium Books' role-playing games are terrible choices for campaigns of political intrigue, and especially so with RIFTS. They are derivative of Dungeons & Dragons, and that is a game build around exploration and high adventure- political intrigue was the endgame, not the game's default mode of play. With that kept in mind, we can make it work- but it won't be easy.
Cloak & Dagger play allows for players to choose to play characters of less-powerful (or less obviously powerful) Occupations and have that mean something. It is a campaign paradigm that favors social skills, interpersonal networks, and other things that Palladium's game engine doesn't do very well. Whether you're taking inspiration from The Godfather, Homeland, Three Days of the Condor, or even Ghost in the Shell (which, for this game, should be the go-to example) you're talking less about payloads and MDC ratings and more about connections and clues. Hell, you might even bother with tools and weapons that don't do Mega-Damage at all.
Because Palladium's game engine is a D&D derivative, your intrigue campaign is best handled as a blend of tense character interaction punctuated by sudden, fierce, and brutal explosions of violence. (Sort of like being on a U-boat during wartime, so go watch Das Boat and you'll get the feel we're after here.) The GM will have to be careful to ensure that attacks vs. defenses are not balanced, but clearly in favor of attacks; the whole idea is that pulling a blaster means You Done Fucked Up up to the moment when shooting is actually a necessary and vital part of the plan (as this sort of campaign does include examples inspired by classics such as Where Eagles Dare and The Eagle Has Landed, as well as the James Bond series).
You will have to account for magic and psychic powers, in addition to real-world tradecraft as applied via speculative technologies. Finding ways to thwart or divert supernatural means to acquire intelligence and properly process it is a thing in a RIFTS campaign, and those who fail to do so lose--and hard--to those who do. (Which, of course, is Yet Another Reason for why the Coalition can't beat Tolkeen as-written.) Making this a major part of a campaign is a very viable initial objective, and should be the go-to option for institutions facing potent supernatural threats of any sort. Plundering real-world tradecraft manuals, existing spy games, and all of the spy fiction (however mundane or fantastic) is necessary for a GM with any serious intention of making this work.
There is another option. This is the Lame Bond Movie option, where you play your bog-standard action/adventure game and just add intrigue bits as plot coupons; add together enough and exchange them for a campaign-shifting event where the players go up against the targeted NPC. You may well be better off doing it this way instead.