Swim straight across the first two rooms you come to, through the current into the square chamber.
Fight the current and head straight across to get to the Song Plant. Then, follow through into the next room, to the right.
You'll have to face a Rotted Core. Shoot all six eyes so that they are all open at once, causing its nut grows out of its bottom. Avoid it's Laser Disco attack by stay between two lasers and spin along with it.
Continue blasting its nut, avoiding any further attacks and shoot the Rotbabies it may spawn.
Once you have defeated it, you'll see a short cutscene of one of three gross flesh barriers disappearing.
Swim to the top left by follow the current through to a room containing a Save Crystal. Make sure to save your game as you're going to defeat another Rotted Core after this.
Go north another two rooms, then right
to come across a bedroom with three pots, two containing the Rotten Cake, Tough Cake, and the last containing some Fleas.
Go back three prevoius rooms, then head down and left,
to a room where you are blocked by a flesh barrier. Shoot the vase to collect the Leeching Poultice recipe that can be use to cure poison.
Go back right, up two rooms, left, down, and left. Down through the strong current.
Shoot the Rotted Core to start a battle. Once done, one more flesh barrier will dissapear.
You can't fight the right current tunnel as it flows upwards. Mark a 'current 2' on your map.
Head down through the left tunnel. You are now back at the start of the Cathedral again.
Head right again, all the way back to where you fought the first Rotted Core. Now take the bottom path.
You'll be shot out into a room full of Merman mutants. Switch to Song Form.
Bind the bloated mutants one by one, out of the way.
Defeat the last Rotted Core.
When you're done, head down through the now open giant scary ominous face gate.