Optional Missions:
Two optional objectives will become available. This is an infiltration mission; you have to remain undetected and avoid killing anyone. You have to knock out the assassins in the area by attacking them stealthily while unarmed. Knock out guards whenever you have the chance and hide their bodies if there are patrols that will be traversing the path; this lowers your chance of being discovered and will make your job a lot easier as you progress.
The first chest should be behind the rock and bushes from your starting point. Swim towards the dirt road nearest to the viewpoint. Hide behind the bushes and knock out the nearest assassin once the patrolling woman assassin walks by. Get her attention by whistling then pull her to the bushes to knock her out. Next, sneak behind the guy standing beside the pile of leaves and knock him cold as well. Make your way to the viewpoint next.
Before heading to the objective, I recommend synchronizing with the nearby viewpoint to help you locate the important items and clear up the map as well. To do this, hide in the bushes beside the viewpoint then wait for the other assassin to walk by. Knock him out then flank the other guy and knock him cold. Synchronize with the viewpoint then do a Leap of Faith to the water to get the first animus fragment.
Follow the objective marker to the southwest while moving through the bushes for cover. Make your way to the beach and knock out the lone female assassin patrolling there. Circle around the next patrolling guard and take him out to reach the chest beside the rocks.
After looting the chest, head to the north. You'll encounter another patrol there; you can just run past or knock him out. You'll find some ruins to the north. There will be three asssassins here; as you get near them, the other two will start patrolling the area. Go through the bushes until you find a fallen tree trunk that you can climb. This will allow you to move above ground using the branches. Get past the patrols by hopping from branch to branch. You'll also get an animus fragment along the way.
You'll have to jump back to the ground at the end of the tree line then climb up on the nearby rock pillar. Hope on the branches of the trees again until you reach the wooden platform. From there, you can hop on another set of branches to reach the next portion of the path. Just make sure you don't get discovered by the nearby patrol. Continue forth until you reach the next area.
You'll find some temple ruins and a lot more guards in the area. There are two chests and a Mayan Stelae nearby. You have to go to the left and get past the assassins. To do this, wait for the patrol to move away then slip through the guard standing by the stairs. Quickly climb up the wall before the patrol turns around and sees you.
Move through the bushes to find more guards along the way. There's a chest is nearby and you have to deal with the guards first before you can loot it. Wait for the patrols to turn their backs and knock out the nearest assassin. Move to the next bush, wait for the patrol to turn his back then knock out cold as well. Finally, time your attack and knock out the remaining patrol away from plain view. After taking care of these three, you should be able to open the chest nearby.
Continue going north then knock out the patrol near the edge of the cliff. Carefully move to the north, towards the Mayan Stelae. Shimmy to the next cliff where there are two assassins. You can lure the roving guard by revealing yourself briefly then hiding immediately in the bush which will prompt him to investigate. Once you separate him away from his partner, you can easily knock him out without alarming the other guard.
The next objective should be very near now. Be careful of the gunner near the objective point since she can see you easily from a distance. Hop on the branches quickly when she's not looking to get close enough for you to knock her out.
You can either lure the nearby patrol towards your position or just sneak past her when she's occupied. If you left the gunner you took down earlier writhing on the ground, the patrol should put her guard down and check her comrade. Use this chance to sneak behind her and knock her out as well. Use the alternate path away from the guards and move along to see James Kidd who's waiting at the entrance of the temple.
You can solve the Mayan Stelae to the west first before talking to him if you want. When ready, go see him to complete the mission.