Ending 1: Imprisoned
After collecting the last of the pyramids at the table, take the Craftman's key and go through the portal.
Insert the key at the top of this mechanism to open it up.
Zoom in on the edge of the table and pick up the metal ring.
Slot it onto the circular plate at the front of the box.
Use the eyepiece to look inside and line up the holes beneath the pistons. Use the lever on the left to switch between the three sections, and rotate the gears with the dial. Press the button once they're aligned.
Back outside, slide the mirror over to the left to redirect the light beam.
Take the second mirror from the compartment beneath the table.
Place it on the inner ring and move the first mirror back to where it was, and out of the way of the beam.
Use the eyepiece to look inside of the Craftman's key. All four beams in here need to point at the crystal. One button rotates the lasers while the other locks one pair at a time in place. Have a tinker - it's a simple enough puzzle to solve.
Enter the train door to finish the game with the Imprisoned ending.