Once the mission starts, follow Kidd back to the jungle until you reach some ancient Mayan structures. This is a tutorial about Mayan Stelaes. The first one of these puzzles that you have encountered is found in Cape Bonavista, during the first game's first chapter. You should know how to solve these puzzles from hereon. Get on top of the stelae and activate it. Align the shapes that will appear using your Eagle Vision then dig on the spot where the lines interconnect to receive a mayan stone. These stones are needed to open an ancient door containing the Mayan Armor. Also, all the other mayan stelae locations will be displayed in the map. Refer to the this page for the individual Mayan Stelae locations.
Follow Kidd until you reach a storage cellar. Go upstairs and you'll be inside a mansion which will serve as your new headquarters. After the cutscene, all Templar Hunt mission locations will be displayed on the map. Completing this missions will award you with a Templar Key, which you can use to unlock the cage in the mansion containing the Templar Armor. Refer to the Extras section of this guide for the individual walkthroughs of Templar Hunt missions.
Once done, leave the mansion and synchronize with the viewpoint by the edge of the cliff to the north to reveal the island and the remaining collectibles. Return to the docks and talk to Kidd to trigger a cutscene. The mission will be complete afterwards.
From hereon, you can now buy upgrades for your new hideout by talking to your crewmates on the dock. You can also upgrade your mansion by interacting with the plans inside the building itself.