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Area that traps you with magic barriers and switches: S-E-W-N
Key Statues- Read their names when you talk to them. Give them the key that matches their color. You'll get 'Submarine Key 1'.
Pentacle- Just keep doing what it tells you until you get 'Submarine Key 13'. (You'll be facing west when you get it)
Go talk to the innkeeper Ertai. You need to steal an amulet from a wealthy Orc to get the shops open. (if you decide to wait at the inn and your hp goes to 0, don't exit! Ask to sleep and your hp will be full again!) You can pay to be able to enter through the Submarine door. (I haven't searched for another way through the door yet.)
After you get the shops open, talk to the potion shop owner. She hints at a mechanism located to the north to activate the bridge to the submarine. (tap the torch on the side of the building in the area where the spike traps are).
The potion shop owner will hint about prisoners near the blacksmith. Tap them to find 'Submarine Key 18'. (The bloody stalagmites are what's left of them)
'Submarine Key 8' is in a fern you need to tap in the area where the "Lower Deck - Right" sign is.
'Key 10' is in a fountain in the room 'Submarine Key 8' opens. (You need to turn the water on to find it).
In the area that 'Submarine Key 18' opens, you need to throw/shoot something at the plants that bounce you back. Find the buttons on each side and press them. You'll receive 'Submarine Key 4'.
The area called, "Play Room" that 'Submarine Key 4' opens, has 7 switches. If you look at the base boards around the wall, you'll see parts are more brown and some are yellow. Activate the switches opposite the more brown colored ones. You'll receive 'Submarine Key 22'.
In the area that 'Submarine Key 22' opens, you need to eliminate the Archer Captain and they will drop 'Key 5'.
'Submarine Key 9' is in the 'Kitchen' on a shelf in this area also. Pay attention to the number of items on the shelves. The shelf with the two items of meat, activate it twice, the switch opposite the shelf with four items activate it four times. It will turn on the fountain.
You'll use 'Submarine Key 9' and 'Submarine Key 5' in the same area. Through a door in the area called, "Armory". You need to eliminate an Archer Guard for 'Submarine Key 16'.
In the area that 'Submarine Key 16' opens, you'll find 'Submarine Key 2' in the fountain there.
In the area that 'Submarine Key 2' opens, you'll need to tap the cracks on the walls to find 'Submarine Key 12'.
After using 'Submarine Key 12', you'll find the "Prison". Search the first skeleton you see inside the door for 'Submarine Key 6'.
In the area that 'Submarine Key 6' opens, you need to eliminate an Archer Guard for 'Submarine Key 7'.
In the area that 'Submarine Key 7' opens, you'll find 6 switches. Look on the floor. Activate the switches on each side of the crack. Leave the switches on each side of the brown patches up. The wall at the end of the hall will open to reveal a shelf. 'Submarine Key 15' will be on the shelf.
In the area 'Submarine Key 15' opens, you'll find 'Submarine Key 11' on the floor in the northeast corner.
In the area called "Medical", that 'Submarine Key 11' opens, you'll find 'Submarine Key 14' on a shelf.
In the area near the "Prison" that 'Submarine Key 14 opens, you need to tap the skull on the wall to find 'Submarine Key 3'.
In the area that 'Submarine Key 3' opens, you'll find 4 switches. Count the blood stains on the floor near each one. This is the order in which you will need to activate them. You will receive 'Submarine Key 24'.
The "Cockpit" area is the area that 'Submarine Key 24' opens.
You'll need the 'Immortal Blade' to cut the green magic barriers down. Clear the area and save the switches for last. The key to the switches is the colors of the flags in the hallway leading to the door and the color of the plants across from the switches. (GREEN-GRAY-RED-RED-GRAY-GREEN-RED)
I don't remember where I used 'Submarine Key 1'!
Edit by Darkstare - Submarine Key 1 opens the second door inside the Cockpit entrance.