It's been awhile, so let me make sure I understand everything correctly. My current mental picture of your vision for Agents of L.O.K.I is something like this:
In Agents of L.O.K.I. you play as Loki Laufeyson the Norse god of mischief who, after his most recent attempt to usurp his foster father Odin, has been exiled from Asgard. Cast into Midgard, he joins forces with Amora, the Enchantress, to track down the infinity stones, collect the infinity gauntlet, and rewrite reality in their favor.
To this end, Loki will need to acquire minions and funds. Minions are acquired either through hiring supervillains at the Bar-With-No-Name (which will involve some sort of dialog tree or minigame for the first time you hire them and thereafter be on “speed-dial”), or by ambushing superheroes (which will involve either combat, paying a supervillain to capture them for you, or both) and brainwashing them to do your bidding via the mindstone.
After recruiting a minion you will, in subsequent interactions with them, have the option to either Corrupt or Seduce them. Corrupting them increases their loyalty to you, basically mindbreaking them to the point where they worship the ground you walk on. Seducing them involves convincing them of the righteousness of your cause with minimal/no brainwashing and leaves their personality intact. Whether you corrupt or seduce minions, and how many minions you aquire, will influence the ending of the game.
Funds are acquired mainly through the Bar-With-No-Name, where you put minions to work as strippers/ prostitutes, as well as sending villains on heists.* With these funds you can hire more supervillains, unlock new rooms/ upgrade your base in Stark Towers, or reinvest the funds into the Bar (i.e. buying better quality liquor, expanding the strip club section, ect.) for better payout in the future. You can also use funds to buy items that unlock extra content (such as gifts for you minions and rival villains, or magic/science devices that summon secret characters) as well as consumables that give you temporary boosts in combat.
Occasionally, either through an automatically triggered event or by choosing to via the menu, you will journey to a fantastic location in the marvel universe in search of an Infinity Stone, or for a side quest. I image these quests as functionally similar to a dungeon in an rpg with several branching pathways, weak enemies that harass you as you progress, a skill or dialog challenge or two, and a big boss waiting for you at the end (usually in the form of a well-known supervillain).
After you have collected all the Stones, or a certain number of Turns have passed, the Endgame will trigger, and you will be forced into a showdown with the BBEG of the game (presumably Thanos, although I could see Odin, Thor, the Avengers, or any number of heroes or villains fulfilling that role as well). After you defeat your foe, you receive an ending based on your performance and choices throughout the game, ranging from pyrrhic victory to complete and overwhelming victory.
*While I don’t believe it’s been explicitly addressed, I assume combat will also give you a small amount of coin as well.