When you arrive back outside after stealing the Arms Flash from Moreau, you will need to make your way across a submerged area. The first step is to jump in a boat, when you will then see a large creature of some sort following you.
Eventually you will reach the other side, and following some cutscenes will need to climb a windmill. At the top you will find a crank that breaks, so you will need to get to the second windmill to get a new crank. Go inside the windmill and climb down the ladder, then head out toward the water.
You will see some submerged platforms, so cross to the next building, then shoot the supports where they have yellow tape on them. This will cause the platform to drop into the water, giving you a way across. Eventually you will come to a raised area with a cart that you can push off into the water. Do this, then drop down to the lower platforms on the left side. Down below you will find multiple switches you can pull that will cause platforms to rise up out of the water.
Head toward the right, pull switches at the Blue and Orange platforms to get all the way across. Be carefully, as some of the platforms don’t stay up for long, so you need to run across as fast as you can.
In this new area are more switches that you need to pull in the following order:
- Dirty White
After pulling them, run back the way you came and cut right down the platforms to keep heading into the submerged area. Follow all the walkways until you get to the end, but be careful. The giant fish Moreau-monster will try to crush you, so you need to time your movements well. Push the cart that you come too down into the water, then drop down and run across to the new area.
You will come to another switch that you can pull which will cause a ship to rise out of the water, and you can then drop down onto it. Make your way through the ship, destroying the green goo, then jump out at the other end. Go inside the new windmill and destroy the lock on the ladder, then climb up and grab the crank. Use the crank to spin the ladder then go to the far side of the platform and climb up to the very top where you can use a zipline to cross to the other windmill.
Crank that one to restore power and then you can return to the pump house and leave the area.