The Crystal Skulls are found at the following locations:
1. After getting the Fire Ninpo, you will come outside to a ledge where you are supposed to jump off and land below to fight more enemies. If timed correctly, you can jump across to the roof on the other side to get the Skull you can see from where you are standing. If you fall short, use the ladder to climb up and try again.
2. The Skull is found next to the first flaming archers you encounter. Run up and jump off the tree halfway down the stairs as you walk towards the bridge they are firing from.
3. Go to the river bed shortly after learning the Water-Run technique. The Skull is resting on the bottom near the end of the river before the bridge. Hold A to dive down and collect it.
4. Defeat the sub-Boss in the room with the giant golden dragon winding around. Go to the second floor, and jump to the platform on the left-hand side. Smash through the wall to find a hidden room with the Skull on one of the shelves.
5. Near the beginning of the sewer area, after learning the Wind Blades technique, there should be a short path to the right with a metal staircase. Ascend the stairs to reach the Skull near the top.
6. After you learn how to perform the Invisible Path technique, go the opposite way of the main path. There is a small crevice in the wall you can run back and forth on to reach a rock platform with the Skull.
7. Go to the streets shortly after exiting the subway. After running for a little while and turning a few corners, you will find an open area and some crowded apartment buildings to your right. There is a Skull on one of the steel apartment exterior staircases/balconies near a ninja corpse. Use Wall Run to reach it.
8. Near the middle of the level when jumping from the broken overpass to a ladder, you should see a ledge with a Skull on it in front of you. Either use a correctly timed jump to reach it, or wait until after you get above that area and climb back down a ladder to collect it.
9. The Skull is on the girders inside the Statue Of Liberty. When you are climbing up the stairs to the saved game point, jump on the girders in the middle of the room. You should see the Skull resting on one of them.
10. Located on a boat in the second body of water you can access. Instead of crossing the bridge, hang left and go around the corner to where you obtain the Kusarigama. Run across the river. The Skull is on one of the boats.
11. Shortly afterwards, you will walk into a marketplace with some tables and chairs with a single exit on the right-hand side. The Skull is immediately to your right outside the doorway you exit.
12. After collecting the Spear Gun and swimming through about two areas, there will be groups of exploding jellyfish creatures. Reach the second group of such creatures on your right in a small passageway. They will respawn for awhile. Keep killing them and collect Essence. After they are all dead, swim over there to find a Skull at the bottom of the floor to your left.
13. At the very start of the level, immediately turn around and jump on the section of roof behind you that slopes down into the water. Cross over to the other side of the roof. Walk down a few step to find the Skull tucked away very close to where you were originally standing when the level began.
14. When you reach the guillotine, cut the rope for the Skull.
15. In the library with a fireplace inside the castle where you fight a lot of ninjas, there is a Skull on one of the bookshelves. It will appear after you make the books fall out by hitting the bookshelves.
16. When you first reach the controls at the front of the ship and start destroying them, a Skull will be uncovered slightly to the left of the main control panel.
17. The Skull is hidden in an alcove on your right after you start walking into a new hallway around the time that you find the Tonfas off a dead ninja. It is near some debris.
18. The Skull is in the snow when you are crossing the minefield. It is found after the first section of mines where everyone was shooting at you through the windows of the three story building.
19. Once you get back inside again and leave the bell tower, you will begin descending a winding square staircase. The Skull is in one of the holes on the wall with candles in it.
20. After you enter the subway, in the room before where you find the dignitary's ID card is a Skull on the right-hand side of the room.
21. The Skull is on one of the gears about halfway up the area where you are jumping from one to another. It is on one of the medium-sized horizontal gears.
22. Go to the big open body of water you reach with the two searchlights. Go all the way to the right-hand corner. The Skull is behind one of the big wooden towers.
23. After using the Jade Mask and entering a new area, you will eventually reach a rope you must use to climb across to reach the other side. About midway through this climb (just past the giant tree), is a branch you can turn and swing towards on your right. Swing to this and then to one more branch for the Skull.
24. After defeating the worm Boss, immediately after the game save is another area with smaller worm enemies. The Skull is on the far right-hand side of this room on the ground.
25. After watching the short intermission sequence with the dead ninjas floating down the river, jump into the water. The Skull is in a small alcove on the left near the bottom, midway to the other shore.
26. After the fight with the worm enemies in the acid pit, use a Flying Bird Flip to reach the area above you. Wall Run on the wall to your immediate left, then jump to the one on the right. Once back on solid ground, turn around and Wall Run one more time from the wall on the left, and jump to the ledge in front of you to reach the Skull.
27. Once you enter the area with many flying dragon enemies, you will quickly reach a path descending to the area below. Once it levels out, follow it around to the left instead of where you normally go. The Skull is on the ground in a small open area.
28. After you pass the second shop, you will climb up a ladder and jump out a window into a familiar village setting from the original Ninja Gaiden. Go to the right of the village, and turn right into a narrow alley near the exit. There is a Skull in the far back right corner of this alley.
29. Pass through an underwater tunnel into a new area. The Skull is in a clearing inside a small wooden structure on the right.
30. Immediately after leaving the ninja fortress, instead of climbing across the rope in front of you, go to your left, and drop down into the opening in the floor. Follow this area back to the beginning of the original game, and jump down all the ramps to the far bottom left to find the Skull.