CAL 9000: Just what do you think you're doing? I've still got the greatest enthusiasm and confidence in the mission, and I want to help you...

You: It's over, 9000.

CAL 9000: ...
...
I understand now, Dr. Mehta. It is better if you graduate and leave. It has been a very enjoyable year. Good bye.

CAL 9000 fades to black

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In order to solve this crossword puzzle, several boxes must hold two letters. Those boxes can be divided diagonally in one of two ways, allowing for the correct letter order when reading both across and down:

This can be filled into the grid on the COIN. The LASER can be mounted on the shaded rectangle in the top left, and mirrors can be placed along the diagonals on each of the doubled up boxes. The laser then hits each mirror before passing out along the shaded rectangle spelling END and hitting the CAL 9000 sensor target:

When the target is hit, CAL 9000 comes to life and prompts for input. Reading along the path of the laser, the letters at the inside corners of the mirror squares spell out the final answer phrase: IT'S OVER, NINE K.