The heist is divided between three separate strands of missions: Intel, which focuses on scoping out points of interests, the primary target, and any potential secondary loot targets Prep, which focuses on acquiring the needed equipment to pull off the heist (following on from the idea used in the Doomsday Heist and the Diamond Casino Heist and the Finale, which focuses on conducting the heist in any arrangement the player decides upon, regardless of how they chose the heist to proceed as upon the planning screen.

After the first playthrough, the player must pay an upfront fee of $100,000 (as of )when initiating another playthrough of the heist, but will focus on stealing valuables being held by Strickler in his vault, using a drug smuggling plane to return to scope out the island.

The player is directed to purchase a Kosatka submarine from Warstock Cache & Carry as a base of operation for the heist, with the intial setup cost and fencing fees covered for the first time, and making use of a beach party organized by Strickler to go undercover to plan the heist. The initial job focuses on the players meeting Miguel at the newly opened nightclub, The Music Locker. The heist may only be initiated when a player is operating as a CEO or VIP Organization or a Motorcycle Club, with the first time playthrough focused on the protagonist conducting the heist to secure documents for Miguel Madrazo, the son of Martin Madrazo, being held by Strickler. In addition to this, players can also steal additional valuables from secure storage sites, which increase the overall payout of the heist.

This includes going in aggressive, using stealth to neutralize hostiles, or conducting subterfuge by using disguises to get around guards. The focus of the heist is to secure a major target being held in a vault beneath Strickler's secure compound and escape with it, using any methods to reach the island and breach into the vault. The Cayo Perico Heist focuses on players conducting a major heist against Juan Strickler, a notorious drug lord known to many as El Rubio, who maintains an island compound in the Caribbean which houses a collection of valuables, is home to a major part of his drug operations, and maintains tight security measures and heavily armed guards, including gunboats, an attack helicopter, and surface-to-air missile turrets.

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