I am stuck trying to get past the 3rd floor door and I've tried everything, everywhere.
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have you tried using your key card with the reader next to the secretary?
Do you have a gaming magazine in your inventory? Find that first, read it and use the knowledge you gained. Then, this magazine will come handy with the retro secretary robot.
If you have managed to open the door, find the three secrets. One is in plain sight, but tiny. The other two have to do with the commander.