Upon waking up, your crew will be concerned. After waving it off, head for the Minister's Office and speak to Avery about the Treasure he mentioned. He'll then give a Puppet Show about Gunn's gold and that you would need to see your respective Pirate Instructor. Go to them and they'll tell you to go to the tavern.

(You can also pick these companions up near your trainers:

Carcarius Grimtooth - Witchdoctor
Chantal Livingstone - Musketeer
Fan Flanders - Swashbuckler
Peter Quint - Buccaneer
The Marchioness - Privateer

I suggest you do as these are the best in the game [Prior knowledge from actual game play] {Notes from Boss (Etta): Chantal and Fan should not be left alone in the same battlefield.})

Upon arriving, you'll be asking for one of the following depending on your class.

Barnabus - Buccaneer.
Ensign Emmett - Privateer.
Louis le Bisque - Musketeer.
Mormo - Witchdoctor.
Sarah Steele - Swashbuckler.

The Barkeeper will send you to the cellar. Head down and witness an argument between your target and Ratbeard. You'll get dragged into a fight before Ratbeard flees and leaves three rats for you to deal with. Fight them before you can recruit the person you were looking for. Run out before stopping by Blind Mew, who will tell you to get the disappointment ship and head for Blood Shoals.

Fly over and speak to Sergeant Muldoon. He'll point you in the direction of the cave, but warn you about the undead. Head in and meet Lasko, part of Ratbeard's former crew. Him and three others were victims of poison from Ratbeard and are in need of an escape. So if you help them, they'll help you.

This is where it gets tricky. You have 3 paths, no order. You must choose one.

Moe: Firecat Perch (Features Crabs and Fire Types)
Manny: Triton's Well (Features Aztecasaurs and Storm Types) (Foreshadow)
Jack: Cyclops Cavern (Features Sharks, Shrimp and Myth Types) (Cyrus Drake is included)

Once you have chosen, you go. You will be doing all three regardless, but you can choose which one is first, second and third. I'll put them in the order of the list.

(Please note that Cyclops Cavern and Firecat Perch run very close to each other. So if you want to do them together, it may be faster. But that's your choice)

~

(Firecat Perch)

You'll be in there briefly to fight some Skarakeet before finding a Chest with a ring for Wilhelmina. Go out to a house where you'll speak to Wilhelmina, who will say that her husband-to-be got taken away.

Go out to the skyway, shoot 2-3 crab ships down before being told to go back to Firecat Perch.

Talk to Private Quinn when you arrive and he'll say that the Crabs were in a house in Perdition's Cave. Battle some undead before breaking into the Crab's base, where they'll tell you that the captain is at the end of the place. As you head there, you'll get jumped by some Fire Elves. Lizzo, a Wizard nearby, will say that Elves got violent for some reason after a performance at the theater. Continue to the Crab's base and barge in, getting pulled into battle. Save and protect the captain before Bonnie claims Parley. Buster Crab will make a deal; Find the Golden Hook and Captain Gordon will be released. He suggests going to Gretta Darkkettle thanks to the Fire Elf problem.

Go to her house, where she will make her complaint before she hears you out. Then she'll make a deal; Get her what she requires for the Fire Elves and the location of the Golden Hook is yours. Enter Perdition's Cave and fight some Rotten Fodders for a Herkimer Stone. Then go to the docks and talk to Gloria Krendal, who will give you some Crafting Supplies for Gretta (Making the note that she knows the witch too well for us to help Gretta hide).

When you return, she reveals that she wanted the supplies first so that you could do one trip. Apparently the culprit behind the Fire Elves and the place of the Golden Hook are the same; The Marie Celestia. She tells you to find Bastilla Gravewynd and collect her Wail. Then you'll have to find the Dutchman and steal the Hook from him.

Head to Perdition's Cave and go to the docks that are there. Fly over to the ship and dock. There are two entrances; a ruined tower and small rowboat. Enter the tower and battle Bastilla for her voice. Then take the rowboat over to the ship and fight your way into the Captain's Cabin, where the Dutchman will be waiting.

Afterwards, return to Gretta, who will use the voice to make a potion and imbue it into your wand. She'll then tell you to go find Alicane Swiftarrow and defeat him then let him know that he is the cure. She'll also tell you not to return to her nor let her name be known outside your crew.

Head up to Fireglobe Theater and battle Alicane. After you tell him about the cure, he'll leave and you'll be able to head back to Buster Crab. He'll thank you for finding the Golden Hook and dealing with the Fire Elves before letting you take Captain Gordon home.

Upon your return, Wilhelmina will be delighted and will ask you to give Moe the good news. He'll be thankful for your doing and you'll be able to tell Lasko.

~

(Triton's Well)

When you enter, you'll meet up with Artur Gryphonbane, who is trying to deal with the storm power problem. Battle some Electric Eels for his sister's wand before finding him with two others.

Apparently this is the base grounds of the problems for Triton's Well. Artur and his sister, Suzie, were looking into the Storm Energy; Duncan Grimwater was looking into the undead problem; Zadok was hunting treasure/looking into the problem up the Well.

Start off by going to Blad Raveneye and get a Lumina Crystal (You must defeat Scarlet Screamers and collect cogs off the ground) before you go fight some Rotten Fodders for Storm Amulets.

Head back to learn that Suzie went to fight the Harvest Lord. While Duncan and Artur have no idea where to look for the sinister undead, Zadok does. He'll say that while he was hunting around, he heard some undead say that "no one will look for the boss with the 'Saurs". He only realized after he discovered the problem up the well that they meant that. Fight some raptors for the Jade Key before Zadok will help you up the well.

Find Itzam Halach and ask for help with finding the Harvest Lord, which he'll gladly help as your target is hiding with their problem. You'll defeat some Tzib'Chac Finskulls for talismans and Kawii Raptors for meat before they point you directly to the Pyramid of Fire.

You'll face the following bosses in order in this dungeon:

Doomhorn
Ch'ai Hulud
Axa Coatl
Blood Lord

At the end, after you smash two of three statues, you'll face Ch'ok Ak'ab and the Harvest Lord. Focus on smashing the Third Statue before turning your attention to the Harvest Lord. This is because the Third Statue will destroy Ch'ok Ak'ab and all Aztecasaurs will leave the battle, leaving the Harvest Lord alone with three minions instead of 8. Defeat the undead lord before Suzie appears, explaining that she discovered the problem with the storm energy. Tell Itzam Halach that Ch'ok Ak'ab was dealt with before finding Suzie at the High Perch where the Tempest Nexus is at.

She'll tell you to go to Halestorm Balestorm and tell him the concern. Mark there before teleporting back to Ravenwood Court so that you can quickly get to the Storm School. After talking to the Storm Teacher, port back to Suzie and calm the Tempest Nexus. Then take her to the Base Grounds, where the others are relieved that the world isn't ending (Yet). They'll tell you that they'll keep an eye on the place. Meanwhile, Zadok tells you to go tell Manny the good news.

~

(Cyclops Cavern)

Upon entering, start by crashing through the sharks in front before meeting up with Nolan Stormgate. He'll explain that between the shady Sharks, violent Minions and Cyclopi, the cavern wasn't safe. He'll ask you to face some Trolls for answers about the other Wizards that disappeared and the other Sharks.

After you learn about the Sharks' plan and what happened to the Students, go back to Nolan. He'll panic before suggesting to warn Cyrus and Mordekai.

Head back and start with Mordekai in the Buccaneer's Den. He'll be alerted by this and will ask you to see Madame Vadima just in case. She'll be stunned by a dark, cloudy vision before giving you a charm to expose the threat. She'll then say that the Sharks are hiding in Perdition's Cave before wishing you luck.

Then go to Cyrus. He'll sneer and bark, but after managing to get him to see the problem, he'll state he can only guide you and that you must find the source on your own. (Please note the line: "Also, make sure young Master Stormgate doesn't get eaten by his own Humongofrog again." It's hilarious.)

Return to Nolan and tell him about what you're after. He'll state that he'll push the minions back and try to deal with the Cyclopi while you go find the students and sharks. (Fun Fact, if you go to these places at selective times while you're supposed to be in the cave, you'll actually find him fighting the Trolls(1), Cyclopi(2) and Minotaurs(3).)

Enter the cave and fight some Rotten Fodder for a talisman. Free the students from the bubbles and send them back to the Cavern. (1: Before you fight, Nolan will be battling the trolls.) Then barge into the shark's hideout and reveal the threat. (2: Before you enter, Nolan will be fighting the cyclopi.) (Also, Shrimp.) Lastly, head over to the Fire Ship and tear it down. (3: Before you board, Nolan will be fighting the minotaurs.)

Group up with the four students, where Nolan will make the remark that you are more skilled than him since he was worn out. He'll add that Akilles' Tower was empty when he checked it in the midst of his minotaur battles. Electra, after she's done checking the other two and makes the comment that he actually did something, will claim that during their kidnapping, she saw Akilles on a ship out to the Forgotten Cove. Nolan will tell you that he'll hold the line while you end this threat. (If you enter the cave, but return seconds later, you'll actually find that Nolan is holding the line against a few trolls and sharks.)

Head out there and up to the top of the mountain to a door. After you break in, you'll be met with sharks and cyclopi guarding a base. Defeat them before using the levers to enter. Once in, you'll discover the Master and the Great One plotting. First defeat Akilles near the entrance before going back and fighting the two corruptors. The Master will be hiding in the back while the Great One roams. Target the Master and the Evil Eye in each back corner of the battlefield to win the battle. Akilles will be grateful and will head for the others.

Once you return, the others will be grateful for your victory and Akilles' help (Nolan had run out of mana and another wave was about to hit.) Akilles will let you know that he will send the good news to Mordekai and Cyrus of the victory here. Meanwhile, head back for Jack and let him know the good news.

~

Finally, after you tell Lasko all three are free, he will give you a clue. The Frogfather knows everyone in the world/skyway better than Bartleby and will know Ratbeard the best.

(Note: some of the Students you worked with can be part of your crew. Please see the side quest "A Wizard's Partner" from the Headmaster.)

Head for Jonah Town and enter the tavern. You'll black out once inside.