Hidden Skulls And Altar Locations:

Blue skull location:

In Act II in Moresby, there is the side quest "Uninvited Guests", wherein the Hero must kill the zombies in Alicia's apartment. Just before entering the room with Alicia inside, the player should enter the bathroom to the right instead. When they enter the bathroom, to the left is a cabinet with a glass door on it with the Blue Skull inside sitting on a shelf. The player must smash the glass before they can pick it up.

Altar

Travel back to the Lifeguard Tower. In the southeast corner of the map there is a bunker that is crowded by a handful of zombies. Following the beach will lead the player to this location.

Kill the zombies and free the survivor. He will then lead the Hero inside. In the main room, there is a manhole cover on the ground to the right, which serves as a portal to another bunker on the other side of the map. Once the player goes through it, they will be in a room with a door to the right and a ladder to the left. The player will need to go up the ladder and pick up one of the red propane tanks and drop it down, placing it in front of the door, and the shoot it to blow up the door. Inside the room, there will be a square indentation on the wall with a skull to the right of it, and an empty space for the skull to the left of it.
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Brown skull location:

The Skull is found 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.

Altar

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.
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Green skull location:

It is found on the south end of the Resort Map, about halfway between the south most bunker and the City Tunnel Gas Station. It is on top of a large rock, which the player will need to jump to get to.

Altar

In Chapter 7, the Supermarket has an aisle full of teddy bears with a green floor. There is also a flashlight shining on a bear. Use the flashlight to see the green arrow pointing on a bear.

It should be noted that it's possible to visit the Supermarket even after the player has completed the quest associated with it. Check the Sewers Map for directions.
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Orange skull location:

In Act II, after the Hero travel through the Sewers and first reaches the Supermarket, at the very first sewage drain that they come across that they have to go down behind it they will find a metal chest and some toilets. Inside one of the sinks will be the Orange Skull.

Altar

It is found in the Sewers shortly before the Hero gets to the City hall there will be in a small room with a centralized trench full of water. Floaters spawn in the area, so the player must take care. On the right side of the room is a drain. At the back of the drain the player will be on a small platform with a single Walker on the ground sitting against the wall, and a door to the left. Go in the door and on the floor of the room behind some soda and boxes is a pile of pipes with an orange arrow pointing right to the top of them. The player will then be prompted to place the skull on top of the pile.
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Purple skull location:

In Act II, as the player travels through the Sewers, they'll come to a room with toxic barrels and a few noxious Walkers, as well as a Floater. There will be a ladder in the middle which they should climb up and follow the path around to the Purple Skull, which rests in front of a shrine. The shrine contains a picture of a woman and her daughter. It should be noted that the player pass through the location a few times during the campaign.

Altar

In Act II while in the city of Moresby, there is a side quest available on the east side of the map called "Uninvited Guests". Once upstairs inside the apartment, the player should head into the kitchen and place the Purple Skull on top of the stove.

Once the player completes the quest and leaves the house they cannot reenter the building. It's recommended to make sure that they have the Purple Skull before they complete the quest. However, it's possible to re-enter the apartment if they avoid talking to Alicia Jacobs in order completing the quest. As of Patch 1.3, the player can return to the altar even after having completed the side quest.