Head down the stairs and into the next room, then activate the door back to the Hall of Doors. Use your flame spell on the cobwebbed doorway to the northeast, then head through.
Defeat all the enemies on the walkway in the next room, then continue northeast through the doorway. Say hi to the Frog King, then continue northeast and grab the Life Seed, then drop off the walkway and head south through the doorway there. You’ll then need to use ranged attacks to trigger the orange plants and destroy the breakable walls in this room. Use your flame spell to remove the cobwebs from the Large Soul Mass in the corner, then use it again to clear the northeastern doorway of webs, then head through it.
There’s an arena fight in the next room — you can choose to use the orange flower at the far end to help you take out the foes. Don’t forget you’ll need to either used ranged attacks or else deflect the projectiles of the little seed pod enemies in order to take them out. Once you defeat the last foe, head up the nearby ladder and free the first of four souls in the Mushroom Dungeon.
Now head out of the arena room back the way you came in, and then exit the room where you set the cobwebs alight via the southwestern doorway. In the next room, head up the ladder in the middle of the room and grab the Life Seed, then go through the crow-sized opening and follow it until you reach a lever; push it to open a shortcut back to the door.
Now go back through the shortcut and drop down to the orange flower. Use it to break the nearby wall, then shoot a flame spell through both firepits at once. This will release the key — grab it and then head through the southwestern doorway.
Fight your way through the enemies in the next room, then head southeast and unlock the locked door. Head on through and you’ll enter an arena fight. You’ll also meet a tricky new enemy: a shield-knight. Focus on killing the other enemies before you take these guys on, then try to only do one or two attacks, then roll away.
Once you defeat the last enemy, you’ll be able to use the nearby vine-ladder to head up and free the next soul. Continue up the stairs and grab the Life Seed, then push the lever — this will open a shortcut back to the Overgrown Ruins (not useful now, but might be later when you return for currently inaccessible secrets). Drop down and leave the the room through the locked door you came in through.
Head southwest and down the stairs, through the two bitey plants, and up the stairs past them. Use the orange flower to break the nearby wall, then continue southwest past the flower and down the ladder. Take the stairs that lead due south, and cross the open gate to begin another arena fight. Once you defeat the last enemy, you’ll be able to take the ladder in the center of the platform up to the 3rd soul, and release it.
Head north back up the stairs, and then head west and over the small bridge. After another brief convo with the Frog King, continue across the bridge and go up the eastern ladder that leads to an upper platform. Head through the doorway to the northeast, then break the boxes and head up the ladder and out the next doorway. Push the lever to open another shortcut back to the door, then go back the way you came and jump down the ladder.
Now you’ll need to light the three nearby firepits in sequence. It can be a bit tricky, but you can always hit the mushrooms for energy and try again until you succeed. Once you’re successful, use the vine-ladder to get back up, then grab the key and use it on the locked door to the northeast and head through.
You’ll run into Frog King again. After he stops talking, use the vine-ladder and head through the doorway to the east. You’ll enter a pretty tough arena fight — focus on conserving your health and being patient. Once you defeat the last enemy, you’ll be able to release the 4th and final soul of this dungeon. Once you’ve done so, head through the doorway to the east.
Climb up the ladder, then take out the enemies tossing projectiles at you. Once that’s done, use a ranged attack on the orange flower to the north to break the wall blocking the 3rd fire pit, then get full energy and use your flame spell to light all 3 firepits in the room. Grab the key and the Life Seed near the broken wall, then jump down the ladder to the west and leave the room via the southwestern doorway.
In the room you released the 4th spirit, exit via the northern of the two western doorways. Grab the Life Seed and break the nearby wall with the Orange flower, then exit this room through the southern doorway.
Head down the stairs and then north, cross the bridge and go up the ladder. Then go past the plants and up the stairs and climb another ladder. Once you get off the ladder, immediately exit the room thorough the doorway to the south. Outside, grab the Large Soul Mass and climb the ladder. Head west and drop down off the ledge, then grab the Large Soul Mass on the shelf you landed on. Then head out the southern doorway and climb the ladder once more.
This time head northeast from the top of the ladder. Pass through the two archways, then climb the ladder and go southeast to the lever. Push it, then jump down and enter the doorway that the lever opened. Continue straight through the next room, then in the following room break the boxes and jump down through the hole behind them. You’ll land on a platform with the Thunder Hammer, grab it! Then jump down and head out the doorway to the southeast.
You’ll find yourself back in the room with the large door, only now it’s powered. Climb up the ladder and head through the door. You’ll be back in the Hall of Doors — climb the stairs to the east and approach the chest to begin the fight to earn your next spell.
This fight is probably the toughest one yet, but luckily you can try as many times as you want. Once you clear the chest battle, you’ll earn the bomb spell, which you can equip with  or the D-pad. Head back down the stairs and break the wall to the northwest, then go up the stairs to the northeast. Continue up the 2nd set of stairs and grab the Large Soul Mass, then drop down (read the book), and break the wall to head back south.
Go back down the stairs and continue southwest by breaking the next wall (break the pots further south if you need more energy, and make sure you have full energy before you take the elevator), then push the lever to activate the elevator back to the main lobby of the Hall of Doors. From the elevator, head southeast and up the stairs, then light the two braziers to open the gate. Head through, and grab the Large Soul Mass and the mini Reaper Door Collectible, and take a look at the book too.
Now head northwest up the stairs and then take the stairs down just west of the smoking crow. Break the wall here with your bomb spell, then grab the Large Soul Mass and the Surveillance Device Collectible, and read the book on the desk. Head back the way you came, and then head east past the smoking crow and up the stairs to reach the main lobby once more.
Head down the stairs to the east, and take the door back to the Mushroom Dungeon. Break the wall in the north of the room to release the imprisoned NPC.
Head through the small passageway in the northwest of the room. Continue through the passageway and down the ladder, out the next doorway and into the large, open room. Head directly west and into the doorway on the northeast wall (a level below you). Head up the vine ladder and through either doorway, then go to the northwestern corner of the room and use your bomb spell to open the wall there.
Head through the destroyed doorway, and in the next room light all 3 firepits as fast as you can. I suggest starting from the top of one of the vine-ladders, then jumping down and lighting the one on the floor, then taking the other vine-ladder up and lighting the final one. Once done fast enough, the gate will open — head through and then through the doorway. Pray the the shrine to get your 4th Vitality Crystal shard, raising your max HP!
Head back the way you came until you reach the room where you destroyed the wall. Leave this room via the eastern doorway, then go up and over the raised platform and down to the other side. Aim a bomb at the wall to the southwest, then run into the hole you’ve made (but can’t see). Grab the Large Soul Mass, then leave the tiny room, then continue out the doorway to the northeast. Go straight through the doorway immediately southeast, and you’ll be in the room with the Reaper Door.
If you’re skipping the secret here, head out the northeast doorway after freeing the NPC, head across the bridge, and into the next room to the northeast to reach the room with the Reaper Door.
Leave the Reaper Door room via the southerneastern doorway, then in the next room continue southwest to the doorway there. Continue southwest straight through the next room. In the following room, avoid the enemies and head southeast to the doorway that the sign points towards. Continue southeast and break the wall blocking your path to enter the Flooded Fortress!