When you are just about to fight Doku, you'll be in the water. By now you should have the spear gun and the oxygen tank. There will be five fish in the area. You can either go to the junction chamber or take the elevator to the Monastery. Instead of going to either place, swim about half way through the tunnel to the junction chamber. Then turn and swim back all five fish will be back. If you kill all five with the spear gun, you'll get around 1000 yellow essence credits per fish. Repeat until you reach 999,999 yellow essence credits. That's as much as you can get. Go through the elevator and the Monastery and then outside to the right is the shop, go nuts and upgrade.