Chapter 1: Sky City Tokyo[edit]
Crystal Skull 1[edit]
Located after first Dragon Statue. Just after obtaining The Art of the Inferno scroll, there is a rooftop across from the room that you are in. Jump across from the right edge of the platform here to the rooftop across.
Crystal Skull 2[edit]
Located after the second Dragon Statue. After fighting the Mage Ninjas in the cherry tree garden, head across the bridge and Then left. Around the corner, there are archers on a balcony and a cherry tree to the right. Do a Flying Bird off the tree to reach the balcony above. It is on the walkway where the archers stood.
Chapter 2: The Castle of the Dragon[edit]
Crystal Skull 3[edit]
Located before the first Dragon Statue. In the river, under the bridge before fighting the archers across the way. It is underwater, but mostly in plain sight. Just after your fight with the dogs.
Crystal Skull 4[edit]
Located after the fourth Dragon Statue. On the upper floor of the room with the golden dragon statue puzzle. In the room adjoining the shrine containing the Vermillion Jewel. Slash the back wall of the room containing the Jewel. Right around the corner, on some shelves, is the Skull.
Chapter 3: Thunderclap of Catastrophe[edit]
Crystal Skull 5[edit]
Located before first Dragon Statue. At the top of the first staircase. Head up an extra flight from the platform that you are required to cross.
Crystal Skull 6[edit]
Located after the third Dragon Statue. When you reach the corpse that holds a scroll detailing Invisible Path Technique, take out the archer in the distance and then perform Invisible Path to land on the platform that he was standing on. Collect the Skull here.
Chapter 4: A Captive Goddess[edit]
Crystal Skull 7[edit]
Located after the first Dragon Statue. After emerging from the underground, this Skull is behind a building, just past some rubble, labeled Coin Laundry. Head around the left side of the building and do a double wall run to reach the balcony that it is on.
Crystal Skull 8[edit]
Located after the second Dragon Statue. After the broken section of elevated highway, there is a hole in the barrier on the right side. The Skull is on a ledge here.
Crystal Skull 9[edit]
Located in the same room as the fifth Dragon Statue. From the Dragon Statue, do a double wall run and try to land on the beams. Head right on this beam and then drop to the beam below. The Skull is here.
Chapter 5: The Aqua Capital[edit]
Crystal Skull 10[edit]
Located before the first Dragon Statue. After obtaining the Kusari-Gama, head down the stairs here and then water run to the opposite end of the canal. The Skull is in a gondola on the opposite side.
Crystal Skull 11[edit]
Located after the first Dragon Statue. After fighting the werewolves in the market, head through the door. The Skull is on a table directly right of the door.
Crystal Skull 12[edit]
Located after the first Dragon Statue. After a batch of Squid Mines, swim into an alcove on the right. Swim down to the bottom and left. The skull is in a cutaway here.
Chapter 6: The Lycanthropes' Castle[edit]
Crystal Skull 13[edit]
Located prior to reaching the first Dragon Statue. On top of the ruined temple roof, on the right side. Head over the first peak and look left and down. The skull is on a ledge here.
Crystal Skull 14[edit]
Located immediately before the second Dragon Statue. Slash the rope on the guillotine in this area to reveal the Skull.
Crystal Skull 15[edit]
Located after the fifth Dragon Statue. In the bottom floor of the library. Head to the rear left-hand side of the room and slash the bookcases here to reveal the Skull.
Chapter 7: The Flying Fortress Daedalus[edit]
Crystal Skull 16[edit]
Located in the same room as the second Dragon Statue. Destroy the consoles here to reveal the skull.
Crystal Skull 17[edit]
Located after the fourth Dragon Statue. In the room after you receive the Tonfa. Head out of the room, head right and then look right past the rubble here. The skull is on the pile.
Chapter 8: Submit, or Die![edit]
Crystal Skull 18[edit]
Located after the first Dragon Statue. After the Rocket Soldiers shooting gallery battle, this skull is located just in front of the building where they were shooting from. It is hard to miss, but it is surrounded by mines, so be careful.
Crystal Skull 19[edit]
Located after the second Dragon Statue. Heading down the stairs after the second belltower. It is in an alcove next to a candle.
Crystal Skull 20[edit]
Located after the second Dragon Statue. Located in the subway car, in the same area as the corpse that holds the Dignitary's ID Card. It is at the back of the room, on the bar.
Crystal Skull 21[edit]
Located after the fourth Dragon Statue. On the gear that you reach after jumping off of the giant Ferris wheel gear. This one is pretty easy to spot.
Chapter 9: Heart of Darkness[edit]
Crystal Skull 22[edit]
Located after the first Dragon Statue. Located behind the rightmost searchlight tower after fighting off the Rocket Soldiers.
Crystal Skull 23[edit]
Located after the first Dragon Statue. When crossing a ravine using a rope, there will be a tree with a branch hanging off it, just before you reach the opposite cliff. Jump off onto the branch and use the series of branches that follow to reach the platform where the Skull is located.
Crystal Skull 24[edit]
Located after the third Dragon Statue. In the small lake with Baby Worms located just after the Dragon Statue, head to the right to a small area of dirt. The Skull is resting on it.
Crystal Skull 25[edit]
Locate after the fourth Dragon Statue. After the cutscene with the dead ninjas floating downstream, jump into the lake here and swim to the bottom. The Skull is resting on a corpse at the bottom left.
Chapter 10: The Temple of Sacrifice[edit]
Crystal Skull 26[edit]
Located after the second Dragon Statue. You can see this Skull resting on a ledge immediately upon entering the room. Perform a double wall run below the ledge, then turn around and perform a wall run off the left wall to reach the ledge.
Crystal Skull 27[edit]
Located after the third Dragon Statue. To the left of the large staircase in the massive room where you fight the Flying Fiends just after the third Dragon Statue. Look over the left side as you descend to locate it.
Chapter 11: A Tempered Gravestone[edit]
Crystal Skull 28[edit]
Located after the second Dragon Statue. After jumping out the upper window of the building containing the Muramasa Statue, head right. Continue past the row of houses and head right. Past the corpse, in the back corner, behind a wheel.
Crystal Skull 29[edit]
Locted after the third Dragon Statue. In the weeded area after emerging from the water. A tiny hut on the right hand side in the first open area here houses the Skull. Smash the door to reveal it.
Crystal Skull 30[edit]
Located after the fourth Dragon Statue. Before crossing the large canyon on the rope, head left and drop into a well. Drop to the bottom, continue ahead and then drop again. When you reach the cliffs, head to the ground level. At the bottom of the cliffs, there is a small room that houses the final Skull. Fans of the series will recognize this as the room where you received Art of the Fire Wheel in the previous game.