When you enter the cistern, go to the right and pull the lever beside the door there. Make your way through and then swim across to the far side. Go to the left and you will come to a locked door with four stones on it. Hit the stones in the order of Top, bottom, left, right (the order can be found on in the main room with the back showing a blue mark, the rear showing a blue mark in a cave and the right hand and left hand both showing a blue mark when closed, in a specific position.) Go through the door and swim over to the vines on the far right. Climb up and then drop off onto the lily pad to the north east of the platform.
When you land, it will spin over and open a passage underneath it in the process. Swim through and spin through the wooden barricades and out through the opening at the end. Climb the vines and you will come to a chest on the other side of a door. Grab the key out of the chest and make your way back to the first room you entered into by hopping off the ledge and going left. Take the water spout up and follow the corridor around to the drop off to the doorway.
When back in the main room, head over to the center and use the key on the locked door. Go through and drop off to land on the floor below. Take out the fancy new type of skeleton and go through the door that opens. Here you will be able to get the whip. Go back out and use the whip on the plug, turning it to release a water spout. Ride it back to the top and exit back out to the main room again.
Make your way to the left of the room, where the red X is on the map, and use the whip on the lily pad near the lever on the wall, to the right of the waterfall. It will flip over giving you a platform to stand on so you can whip the lever. Do so and then jump down into the water and swim through the open fish mouth. Enter the next room and kill the spider. Once its dead, go to the barred gate and whip the lever through the bars to open the door.
Enter the next room and clear out the enemies. There is a wall to the left that you can use the harp with to reveal a symbol for healing. (hint: if you draw a heart with the sword on the wall, you get full health recovered.) Make your way up the right side of the room and use the whip to swing over to the vines. Drop down and then jump up onto the spinning cylinder. Ride it for a bit then drop down and you will then be able to whip another branch.
Do so and swing from the branch to the lever on the wall. Pull it to open the bars to the right and then climb back up the vines behind you and swing up and through the open doorway. Once through, take out the Baba’s and then whip the plug to drain the water in the center of the area. Take a dive into the center and you will enter in a new area with a spider coming to greet you, Save there and then use the Hook Beetle to snip the spider webs, sending the spiders into the water and revealing a passage at the same time. Swim through the small opening and climb up the right side. Whip the Bokoblin on the other side of the bars and you can snag the key off him for the door on the other side of the water. Jump in the water after opening the door and it will take you to another room full of lily pads.
Swim to the east side and jump out to the ledge there and whip the pad next to the vines so you can get on. Climb up and then follow the stairs to the edge. Jump off to the pad below that is in the center of the room to tip it over and then swim through the new opening. Follow it around through a tunnel full of Froaks and you will come to a ledge in the same room but on the other side. Whip the plug there and a water spout will rise in the center of the room. Make your way back down into the water, up the vines, and up the stairs again to the ledge you were at previously. Whip the pad and flip it so you can now hop across to the other side and up the stairs to get outside.
Climb the vines to the left of the doorway and you will come to a plug and a level. The lever lowers a doorway and the plug will spout water near where you entered. Head back to the right by diving in to the water. Climb up on the far ledge and then whip across the branches along the north wall to reach a chest and open door. Inside the chest is the Dungeon Map that show a purty green flame on the map. Now make your way back into the center of the area, back through the door you went into earlier that leads to the very top and very bottom. Drop all the way down to where you got the whip and go through the door there that is now open. It will take you to an underground place that is full of…zombies.
Make your way through the bodies and you will eventually come to the main area. Go up the right side and there will be a river of pink liquid to the right. Hop across the pads and turn around to see two large blue eyes staring at you. Send the Hook Beetle through to hit the pink diamonds and that will stop the waterfall of goo. Hop back across and follow the path north as far as you can and then send the hook beetle to grab the flower bomb there and carry it across to the pile of rocks on top of the pillar under the branch. Hop back across the pads and use the whip to swing from the now accessible branch to the spinning vine pillar. Climb to the top and hop the next one and then to the ledge below. Jump to the wall of vines to the right of the white sheet and whip the lever there to reverse the direction of the very fast spinning platform below.
Hop down to the top of the circular platform now and ride it to the other side. Hop off at the far end and follow the path to the next spinning pillar. Climb it and hop off on the other side. Jump to the vine wall and now you will need to reverse the hook, to spin the pillars the other way. Do so and hop down and jump to the spinning pillar and drop off when the ledge arrives below you. Now follow the path upwards to the large open area. Drop down and a ton of zombies will attack. Finish them off and then climb the thread in the center. Climb it all the way to the top and then pull the lever on the wall when you reach the top. When the platform appears, hop on it and whip the hook upwards to raise the statue.
Climb back down the thread now and return to the point where you entered the area to find a chest that contains the Blessed Idol, which is the golden key needed for the door at the very top of the center area. Once you grab it, zombies will appear and the statue will start to lower again. Run up the hill to not get squashed and then enter the door that is there now. Ride the water spouts to the top and use the key on the mechanism at the very top to open the ceiling. Run up the stairs and whip the 4 plugs there and the statue will rise some more. Once it stops, run up the stairs and you will have a little battle with a feller named Koloktos.
To defeat Koloktos, you need to run around him and wait for him to smash his arm down on the ground. When he does, target his arm joint with the whip, and pull it out of its socket. Keep repeating that until he only has two arms left. At that time, the red core on his chest will be exposed and you can run up to him and target it. With it targeted, slash at it as many times as you can and he will then pull his arms back together. Repeat that a second time and then Koloktos will change form, but the same rules will still apply. In his second form, use the pillars for cover from his attacks. When his arms slam the ground, use the whip to pull his arm out and then pick up his huge sword. Once you have it in your hands, run up to him and slash at his legs and then body and finally the red core. You will need to repeat this once more, but once you do, he will be down for good. Make your way back out with your fancy new sword after visiting the flame and you’ll need to go to the Thunderhead again.