I'm playing the TEAM path.

Hint 1 of 12:

First of all, you should know that you can't operate all of the
controls until you get rid of Sophia's guard.

Hint 2 of 12:

There are four controls.  Two require puzzle solving to reach.

Hint 3 of 12:

For example, you need to unlock the rudder control.

Hint 4 of 12:

You'll have that key once you find the stones.  See another question for
more details.

Hint 5 of 12:

To fix the depth lever, you need to find a replacement stick.

Hint 6 of 12:

There's no real logic to finding the part.  Try anything that makes sense.

Hint 7 of 12:

Use the plunger from next to the Nazi guard.

Hint 8 of 12:

Now you should be able to find all four controls.  There are two in the
aft section (reverse, speed) and two near the sub's center (depth, rudder).

Hint 9 of 12:

There is an entrance to Atlantis on the left side of the screen.

Hint 10 of 12:

You need to change your depth, direction, and position (back or front of
the screen) to get to it.