The Skull is found in Bunker #02 in the Resort area. During the mission "Black Hawk Down", the player will come across a helicopter passenger named Nikolai. After taking him into the bunker, they should head to the back room where the workbench is and on the right access the portal to get into another bunker. Once inside in the back there should be a Suicider. Kill him and search the room for the Skull.
When looking for the Altar, the player will have to climb the rock mountain on the east coast of the island and reach the very top. From the Lifeguard Tower they should go towards the first underpass of rocks along the beach and find planks of wood leading up. As soon as the player gets close to the arch and turns around they should see a brown arrow pointing up. There will be a couple skulls sitting on the rocks near a flag. This is where the Brown Skull must be placed.