Banjo-Tooie/Jolly Roger's Lagoon
As you enter here, walk up the monument in the center with the words Jolly Rodger's Lagoon on it. Shoot a grenade egg to uncover the split pads.
Use the Mumbo Pad to oxygenate the water so you can't drown. Jump in and dive down to the deep water.
Use the split pad at the entrance, and take Kazooie to get Wing Whack (265 notes) at TurtleView Cave. Take her to the area near Mumbo's Skull and blow up the dirt mounds with explosive eggs. Use the Flip Flap to reach the doubloons in the cave above.
Orange Jinjo: after you get the Running Shoes from Captain Blubber, use shoes and run across the lake to the Jinjo in the cave. This should be the final Orange Jinjo, rewarding you with a Jiggy.
 Deep down
You'll see notes inside the sea anemone tentacles. Shoot their eye with a regular egg then grab their treasure.
In the tunnel down below there will be an octopus swinging its tentacles. Use an ice egg on the octopus's head to freeze it. Swim past to reach Atlantis.
There's another tunnel with blue light at the end. That leads to Smuggler's Cavern.
You'll find treble clef (20 notes) in the anemone to the left. Head to the pillar on the right and activate the warp pad. To your left in the rocks is the second empty honeycomb, hidden in a tiny alcove to the right of the temple. Turn right from there and get 10 more notes, then enter the building.
 Electric Eel's Lair
Swim up to the top to get Talon Torpedo for 290 notes. You can now break open waterlogged rocks and doors with Kazooie's face on them. Return to Atlantis.
 Jiggy #2
Swim up and use Talon Torpedo to snatch the Jiggy from the translucent fish. You can also kill puffer fish with this attack.
 Temple of the Fishes
Go up to the green broken temple and read the symbols above the door, then go to the center of the room and shoot eggs into the corresponding baskets of the stone mermaids. The order of the symbols changes with each game.
Inside you'll have to play a minigame with a new acquaintance, Chris P. Bacon. Help protect him from the attacking fish so he can photograph the paintings on the walls. You'll have to keep him from being bit for 1 minute. Make sure you have full grenade egg ammo, then start the event and swim to one of the walls while staying near the surface. You should be able to
 Seaweed Sanctum
Red Jinjo on the third floor corner pillar. Backflip up to get him.
 Sea Bottom
Head into the water and activate the warp pad down to the left. Use grenade eggs on the big orange fish's teeth as it swims around. It can't hurt you. After they are all destroyed it will leave its mouth wide open; swim inside.
 Inside the Big Fish
Shoot the Big Fish's teeth first, until all of them are gone. Then enter the Big Fish's mouth. Head down the left tunnel to save Merry Maggie who will return to Jolly. Visit Jolly's to receive a Jiggy. Purple Jinjo at end of right tunnel.
 Empty Honeycomb #3
Take the green tunnel past the octopus. Use Talon Torpedo to get the third and final empty honeycomb.
Take the lightblue tunnel past the octopus, break the box and grab the fourth Red Jinjo. Destroy the silver Kazooie face blocking the Water Supply Pipe. Use ice eggs to freeze the fans. Head to the end the tunnel and go through it. Grab the White Jinjo (free Jiggy) standing there, then climb the pipe and return to Atlantis.
Head down the tunnel to the right of the warp pad (sort of white). In the next room go to the bottom and grab the Glowbo. Surface and give it to Humba Wumba.
 Torpedo Action
As a submarine, head to the lockers area and go to the end of the room and into the dark hole. Play the minigame to get a Jiggy.
 Boss Fight
Head back to the locker area and enter Davey Jones' Locker to fight the boss, Lord Woo Fak Fak (Self Important Angler Fish). It does not hurt you to run into him, but look out for the sparks he fires. You can beat him by shooting gernade eggs at the boils on his sides. After you hit one, the next one will be flashing. After six hits, his eyes will open and become the new target. Six more hits are needed to finish him off.
 Smuggler's Cavern
There is an aggressive puffer fish here that can't be killed with eggs so watch out. There's also a transparent fish with a cheato page inside. You'll see a Kazooie only metal tunnel.
There's a jiggy here on a platform above the surface.
Go up the trail and through the door into Jolly's. Use a grenade on the gunpowder keg to blow open a hole to easily return later.
 Empty Honeycombs
Backflip onto Jolly's tavern sign. Use the Jumpad on the chimney to grab hold of the cliff. Sidle past the two snappers, and drop on the upper pipe to grab the first Empty Honeycomb.