It is actually possible to get out of the giant manatee by collecting 100,000 grubs for an artificial cochlea, as suggested by Coronado Da Cava. It can take a lot of time (although a cheat code is available), but if the player succeeds, the game will skip to the part where the ship resurfaces again. Even the items that would have been obtained while following the intended way (i.e. obtaining the original cochlea) will carry over.
Inside the giant manatee, Guybrush finds a portrait of 'Fisheyes' Alabaster. Upon asking, Bugeye will tell Guybrush that Fisheyes is their inspiration for mutiny; he was a professional lookout, but the strain of the job cost him his eyesight, after which he decided to never work another day in his life. The original script contained a much longer backstory for Fisheyes: he joined an expedition led by an "egomaniacal explorer" who left his crew to their demise during a pirate ambush. When the gun that Fisheyes used to defend himself exploded, it caused his eyes to "roll to the side of his head for the rest of his life". Losing everything he had, Fisheyes became an inspiration for mutiny by warning other young adventurers not to put their fates at the whims of an explorer. The creators at Telltale Games deemed this backstory a bit too dark and long, so it was shortened.
Every time you check Guybrush' file inside De Cava's file trunk, the information on it changes. For example, his expertise can alternatively display 'Ghost pirate removal', 'Voodoo doll assembly', 'Monkey-tamer and thrill-seeker' or 'Mighty piracy'.
Moose refers to the drinkable body fluids of the manatee as 'ichor'. According to Greek mythology, ichor was the blood of the gods, an ethereal golden fluid that made them immortal.
LeChuck mentions that "there's something about the open ocean that makes a man feel alive", a pun on his quote from The Secret of Monkey Island (1990), "It's days like this that make ye glad to be dead"