There is one in the lower courtyard near the rocket part for the rocket shield, just outside the gate trap/Double Tap. There is one in the building above the Undercroft (0G Room), opposite where the electric trap is. There is one inside the Undercroft (0G Room), on the opposite side of the wall where PAP is.
In order to complete the upgrade quest, you cannot pick up any new upgrade quest items.
The first one is directly beside the clock tower outside the map. The next one is east to the KRM wall buy. The final one is at the rocket pad, with a bunch of sticks on top of a stone slab.
If the pyramid is not turned on, the low gravity cycles will not occur. To turn on the pyramid, stand on the 4 blue pyramid symbols in the undercroft. [1] X Research source
In the small room above Double Tap. [2] X Research source In the lower courtyard, near the jump pad and build table. The final one is in the rocket pad near the teleporter.