You went through the Cyan door with Alice and chose to betray her, then you went through the green door.
There are four books on the bookshelves that you need to take out. They are brighter colors than the rest of the books. There is a light blue book called The Stairway, an orange book called And Lion, a green book called To The Sun, and a red book called Go Up.
Find the locked box in the corner. Take the green die from the top.
Go to the desk. Get the blue die, the ink bottle, the music box, and the notebook paper.
Go to the scale in the corner. Open the drawer to get a screwdriver. Remove the red die and the 50g weight from the scale.
In your inventory, combine the screwdriver with the music box to get the cylinder. Combine the cylinder with the ink bottle. Combine the inky cylinder with the notebook paper. The piece of paper is stored in the Archive.
Use the weight on the scale. You have to weigh the dice. The result is that the red die weighs 50g, the green weighs 100g, and the blue weighs 150g.
The locked box shows the blue die plus the green die times the red die. However, if you go from left to right, you will get the wrong answer. You have to start by multiplying the red die times the green die. That's 50 x 100 = 5000. Then you add that to the blue die. That's 5000 + 150 = 5150. The padlock code is 5150.
When you unlock the locked box, you find a book that contains a bookmark with a colorful pattern on it. The bookmark is put into the archive.
Put the Books on the Shelves
You took four books from the bookshelves. Now you have to put them in the
correct places on the shelves. Look at the back cover of each book. It has
a book title, and a letter/number code. For example, one book says
TO THE SUN
on the back. This means that you have to put the book titled TO THE SUN on shelf C-05-18.
Look at the computer screen in the middle of the room. When you are looking from this perspective, the shelves from left to right are A, B, C, D.
The next number in the code is the row that the book goes on. Start counting from the top of the shelf to find the correct row (it will be a row with an empty slot).
The third number is the column. Count from the left to find the place to put the book (it will be an empty slot).
Once you have put all four books in the correct places, the bookshelves are lowered to make stairs. The girls make Sigma go up there because he's being lewd. Take the stuffed lion doll.
Get the Escape Password
In your inventory, examine the lion to get a memory card. Put it into the computer in the middle of the room, then touch the screen.
This is a dice puzzle. If you took the cylinder out of the music box with the screwdriver, used the ink bottle on the cylinder, and used the inky cylinder on the notebook paper, look at the resulting pattern, and also look at the colorful bookmark. If you put the dice into the correct pattern such that the colors match the bookmark and the pips on top match the pattern on the notebook paper, you will get a safe code.
Get the Secret File Password
Now do the dice puzzle on the computer again, but this time just put the correctly colored dice into the positions from the bookmark. The pips on top don't matter. This gives you another safe code.