The Empty Boxes are 'effects' in the Rust chapter that you find in three places that were previously inaccessible in the school, corrupted alleyway hospital, and within Oreko's hidden lab in the Industrial Maze. Naturally you can only get them after discarding all your effects and becoming Rust.
Also please note that these boxes like the effects do not need to be collected in any specific order and thus you could collect them in any order you want.
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 > Pipes and Phone Poles > Apartments 1 > Isometric Pathway > Apartments 2 > Sugar Hole (back) > Alleyway Hospital > Corrupted Alleyway Hospital
- Video: http://www.youtube.com/watch?v=pmkXNHJ150M
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 & Blue Passage > Hospital > Bone Maze > Red Body > Sewers 2 > Industrial Maze > Orange Staircase > Industrial Maze (Oreko's Hidden Lab)
- Video: http://www.youtube.com/watch?v=uG0Kw-ZcmrE
Empty Box 3 - The School
This last box is found in the basement of the school. Previously the room down there was blocked off my red static but going into the room is now possible as Rust. 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're moved back outside the room.
- Nexus > Neon World > Red & Blue Passage > Hospital > Bone Maze > Red Body > Sewers 2 > Rusty Pier > Slum > School
- Video: http://www.youtube.com/watch?v=8qo6cqouxLQ
- 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.