These are necessary to unlock the True Ending, and like the effects, you do not need to collect them in any specific order.
Empty Box 1 - The Womb
This one is found in the area exactly like in the Dying Girls Event and by interacting with the giant black haired girl on the wall. However unlike the passage to the dying girls event where you had to kill the black haired girls to create a path these ones will all explode simultaneously.
- Nexus > Pipe World > Apartments 1 > Isometric Pathway > Apartments 2 > Sugar Hole (back) > Hospital > Parade Ward
Empty Box 2 - The Tube
This is obtained by interacting with the tube housing the giant Sabitsuki in a secret lab in the Industrial Maze. Getting to this room requires going though the Orange Staircase which previously was a dead end until you reach the bottom and go through the machine.
- Nexus > Neon World > Red and Blue Path > Hospital Maze > Bone Maze > Red Body > Sewers 2 > Industrial Maze > Orange Staircase > Industrial Maze (Oreko's Hidden Lab)
Empty Box 3 - The School
This last box is found in the basement of the school, previously blocked off by red static. Interacting with the giant smiling mouth on the wall will grant you this last box and with that, a sinister laugh is heard and you are back outside the room.
- Nexus > Neon World > Red & Blue Passage > Hospital > Bone Maze > Red Body > Sewers 2 > Rusty Pier > Slum > School
- They still show the 'get' when you collect them, even though the box itself is empty.
- The three empty boxes may be related to some of the most traumatic experiences Sabitsuki has had.