Leave the ferry and head to Steiner's workshop. There, you find Sara - tell her about the situation and you will receive a crank.
Go to the basement where in the center you can find a ferry model. Zoom on the model and at a small lever (on the right) in the stand on which the model stands. Next, switch the light on (move the small lever from right to left) so you can see the model better. Zoom out and place the crank into the hole in the longer side of the stand (while zooming in). Then, turn it right (make the correct move with the mouse) so you can remove the metal rods around the model.
Take a look at the plate about the Krystal, fixed to the stand. Then, zoom out. Now zoom on the ferry's right broadside. You must point the correct numbers in the right order by using the dial on the left. By doing that you can extend almost the entire chain hanging on the right (the one next to the "Krystal" name written on the broadside).
Get the key from the ferry's model
The text engraved on the plate is a hint that can help you in finding the right numbers - the numbers 98, 60, 80 and 30 and the sentence that says that sometimes you need to go back. The code for the ferry's model is 30-80-60-98. Start with the number 30 (by making a proper move with your mouse while holding LMB move the pointer at 30 and then allow it to go back to the beginning) - the chain will lower a little bit. The pointer should be moved slowly so you won't go too far and miss the number that you want to point at (when this happens the chain goes back and you must start from the beginning). In the case of the last number you must go beyond 90 on the scale (all the way).
When the active point appears on the chain you can pull it which raises the quarterdeck's roof and reveals the hidden miniature Krystal's ignition key. Take it (while zooming in).
Now, by using the acquired template, you must make the ignition key that has the right size. Go to the table on which Kurk's prosthesis was previously lying - right from that place, left from the projector, you can find the machine that makes keys. Zoom in at it and from the small box on the lower shelve you must take (while zooming in) a raw key. Zoom out and look up so you can see the device clearly (but don't move the camera too high because when you zoom in the active points can be outside of your frame).
Create a spare ignition key
When zooming in look at the chamber on the left. When you zoom in again open it (move the mouse from right to left) and in the center place the miniature ignition key. Move the button on the left (move the mouse downwards) so spikes can come out from the borders of the half-circular plates. Close the chamber's cover (move the mouse from left to right). Zoom out and take care of the right chamber. Open it while zooming in (move the mouse from right to left) and place the raw key in the center. Close the chamber's cover (move the mouse from right to left) and stop zooming in at it.
Now, by turning the crank on the right side of the device, set, on the percentage scale, the size of the key in relation to the miniature template. 100% means that the created key is the same size - because the miniature from the ferry's model is smaller than a real key you must choose a bigger scale: 150, 200 or 250%. 200% is the right choice - on the key you can see the indication saying 50% (you can check it in the equipment) so if the key is smaller by a half from the original then the original is 2x bigger then it. By turning the crank (move the mouse properly) move the round pointer at 200. Lastly, start the device by using the red bolt on the upper right (move it up and down). When the machine stops working (Time to collect your thoughts achievement) you can zoom in and open the right chamber and take out the duplicate of the Krystal's ignition key (if the key has the wrong size you can take another raw key from the shelve and start again but if you did it on your first try then you receive Master locksmith achievement).
Return to the ferry, and then go to the bridge. Click on the ignition (the top socket in the column left of the steering wheel; you will receive the achievement Mechanical Awakening).