Start at the first Tyne Wellspring inside The Architect. Head left and follow the mechanical turtle up.
Use your claw to frighten the turtle to your right. This will turn off the purple beams.
Head up and fight the enemies that spawn.
Go to the Tyne Wellspring on your right.
Keep going right to the end of the hall. Use the sub to trigger the sensor in the middle of the room and exit the sub.
Swim down and scare the yellow turtle, then return to the sub.
Head left and take the next tunnel down.
The red turtle will trigger an alarm and restructure the entire map.
Head left from that room to the Tyne Wellspring and sensor. Use the sub to trigger the sensor and exit the sub again.
Swim up and right.
Wait for the turtle to trigger the blue sensor and swim through the gap in the blocks.
Scare the turtle and drag it down. Place it over the sensor and get back in the sub.
Head left and down. Use your magma bomb to destroy the ice gate.
Weave your way through the purple beams straight down for a silver treasure, then swim along them to the right to the next Tyne Wellspring.
Head straight up when you see a gap in the beams and scare the turtle you find there. Drag its shell straight up and place it on the first sensor you see.
Fight off the enemies that spawn, then park the sub on top of the other sensor to let Merryn get out and grab the silver treasure.
Keep heading up and use another magma bomb.
The red turtle will rearrange the entire level again.
Head left and use Merryn's knife to direct the blue beam into the sensor on the ceiling. This triggers a white beam that hits the turtle on the left.
Head to the left and use the sub to open the gate in front of the red turtle. Get out and direct the green beam into its sensor to damage the turtle again.
Head down to the bottom left room. Use a magma bomb to simultaneously free and scare the turtle on the left.
Drag its shell up to the sensor above you. Use the sub to trigger the other sensor to move the red turtle into the top right room. Use Merryn's knife to reflect the red beam and hit the red turtle again.
Head right and straight up to claim the Sonar Blast.
Head back down and use a Sonar Blast to break the glass wall below you.
Use another blast to break the wall to your right and enter that room.
Head through and use another Sonar Blast on The Architect's control dome to free yourself from The Architect.
The reversed currents will push you back down on top of Merryn's father's boat where you can pry open the roof and grab Merryn's father's journal.
Before you get to read it, a giant squid will grab you, drag you to the ocean floor and into a long cutscene.