Escape the cenote then head out. Kill the guard outside then grab his weapon. You don't have your weapons with you so you need to follow the trail and eliminate the guards silently. Upon reaching the pirate base, you have to eliminate the targets stealthily; otherwise, they'll trigger the alarm and you'll have 5 minutes to reach the chopper.
Take your time and eliminate the enemies, especially the snipers and RPG troopers. There are two snipers near the chopper as well as a sizable number of enemies including a heavy and a guard dog. If possible, try to kill the RPG trooper in the first area and get the RPG to instantly kill the heavy. Climb the chopper for a scene.
Escape from the mass grave then sneak into the nearby pirate camp to get your stuff back. Your equipment is located in the far northern shack where a heavy is patrolling. The mission will be complete as soon as you get your equipment back.