Your OT-2 has:
A removable top window.
Removable covers for the holes in the left, right, and rear windows.
Installing these is optional, but they can help stop cross-contamination from entering and leaving the OT-2.
Install the top window
Top window (set aside during unboxing).
Top window screws (from your OT-2 accessory kit).
2.5 mm screwdriver (from your OT-2 accessory kit).
Slide the window onto the top of the OT-2:
Open the plastic bag for the top window screws:
If the screws don't already have washers and O-rings, insert them:
Screw the 4 screws into the corners of the top window:
Install the window covers
The left and right side windows of the OT-2 have holes at the bottom.
Depending on when your OT-2 was manufactured, the rear window might have a hole, too.
You can use the included side window covers and rear window cover to cover them up. (You found and set these aside when you unboxed your OT-2.)
The window covers snap on magnetically. Attach them to the inside of the OT-2.