Guybrush arrives on Phatt Island to look for the map piece of Rum Rogers Sr., First Mate of Marley's pirate crew. However a guard recognizes him from a "Wanted!" Poster and he is quickly arrested and taken to Governor Phatt, a morbidly obese bedridden man. After a short conversation, the governor has him thrown in prison to await his collection by LeChuck. Guybrush escapes his cell by getting the guard dog (who is holding the key ring in his mouth) to come closer to grab a bone.
Back out on the island, Guybrush tries to reach Rogers's hut, but finds that the way is blocked by a large waterfall. Searching the area he finds a valve controlling the flow of the waterfall, but has no way to shut it off. Back in the Scabb Island tavern Guybrush finds a monkey playing the piano, which he hypnotizes by placing a banana on its metronome. He takes the monkey back to Phatt Island and uses it as a monkey wrench to turn the waterfall off, opening the way to Rogers's hut.
Guybrush finds the hut inhabited by Rum Rogers Jr., Rum Rogers Sr.'s alcoholic son. Rogers refuses to discuss anything until Guybrush defeats him in a grog-drinking contest, but the stuff is too strong and it knocks Guybrush out. Guybrush returns to Scabb and asks the barkeep for some Near-Grog, but discovers that the entire stock was bought-out by one Captain Kate Capsize. Guybrush finds her on Booty Island, but she refuses to sell any Near-Grog to him. Guybrush takes one of her flyers, bearing her portrait, and plasters it over his own "Wanted!" Poster back on Phatt Island, which gets Kate arrested. Guybrush then steals the Near-Grog from her confiscated possessions.
With the Near-Grog, Guybrush returns to Rogers' hut where he switches the grog for Near-Grog and wins the contest, drinking Rogers under the table. Exploring the hut he discovers a wall of loose bricks that can be pushed to open a trap chute leading to a secret chamber underneath the hut. Unfortunately, he does not know which brick to press, and ends up being ejected out of the hut each time.
Guybrush decides to look instead for Rapp Scallion, the pirate crew's cook, who is said to have opened a wiener shack on Scabb Island. He finds the shack, but the door is locked. Guybrush learns that Scallion died and was buried in a crypt at the Scabb Island Cemetery, but the crypt is locked as well. Guybrush travels to Booty Island and finds the crypt key at Stan's Recently-Used Coffins store. He tricks Stan into demonstrating one of the coffins and nails the coffin shut, stealing the key and escaping the area. Back on Scabb, Guybrush enters the crypt and uses some magic Voodoo powder on Scallion's remains to bring him back to life temporarily. Scallion only asks Guybrush to check whether he left the stove on at his wiener shack, after which he gives Guybrush the first piece of the map.
Guybrush finds another map piece, belonging to cabin boy Young Lindy, at a memorabilia shop on Booty Island. Unfortunately, the proprietor refuses to part with it for any reasonable sum of money. He agrees to trade the map for the figurehead of the Mad Monkey, which sank somewhere in the vicinity. Guybrush travels back to Phatt Island and registers at the local library to find a book detailing the exact location of the Mad Monkey wreck, and decides to charter the now-released Captain Capsize's boat to go looking for it. To finance the voyage, Guybrush enters a long-distance spitting contest, wins it by cheating with the help of some phlegm-thickening juice he purchases at the Scabb Island tavern, and sells the trophy plaque for the money. With Kate's boat, Guybrush reaches the Mad Monkey wreck and dives down to retrieve the figurehead, trading it for the second map piece.
The last map piece belonged to Horatio Marley, grandfather of Elaine Marley, and is kept at her mansion on Booty Island. Guybrush attempts to visit the mansion, but is stopped by a guard who says that there is a costume party happening at the mansion and only invited guests are allowed. Guybrush tries to purchase a costume at the local costume shop, but is told that all of the costumes are reserved for the registered guests. Back on Phatt Island, Guybrush encounters a back-alley roulette game whose operator claims to offer a costume party invitation as one of the prizes, but Guybrush just can't seem to win anything at all. He observes another player who keeps winning, and follows him to another alley where the man knocks on a door, answers a strange question involving hand signals, and receives the next winning number. Guybrush deciphers the code and gets the winning number himself, finally acquiring an invitation.
Back on Booty Island, Guybrush takes the invitation to the costume shop and receives his costume - a pink dress. He wears this to enter Elaine's party, and quickly sneaks his way to her room to steal the map piece. As he tries to leave the mansion, Elaine's dog (whom she's named Guybrush) smells him and alerts the guards, who arrest Guybrush and take him back to meet Elaine. Turns out that Guybrush and Elaine dated for a while, but he was a jerk and angered her greatly. Guybrush tries to sweet-talk his way back to Elaine's good graces, but he fumbles and lets slip that he's actually really just interested in the map. Elaine throws the map out the window in anger, telling him that if that's all he wants, he can have it.
Guybrush rushes out to the mansion grounds, but the wind picks up the map and carries it away. Guybrush rushes after it, but finds the map stuck in a branch on the side of a steep cliff. Guybrush returns to Phatt Island where he had spotted a fisherman earlier, who agrees to wager his fishing rod if Guybrush could catch a larger fish than he could. Guybrush steals a large fish from Governor Marley's mansion, winning the rod. However when he tries to fish the map off the cliffside with the rod, a seagull arrives and carries it away.
Guybrush chases the seagull and arrives at a giant tree. The tree has a spiral of holes running up its trunk, with little planks stuck in them to serve as stairs - but one plank is missing. Guybrush steals an oar from Marley's mansion and sticks it in the hole to serve as the missing step, but when he steps on the oar is breaks and Guybrush bangs his head as he falls to the ground. While unconscious, Guybrush has a strange vision of his parents, who turn into skeletons and begin to dance while singing the song "Dem Bones". Guybrush is excited and writes down the lyrics on a napkin as they sing. Suddenly, LeChuck appears out of nowhere, scaring the skeletons away. He gloats to Guybrush that he cannot be killed at all, and then turns into a younger version of Guybrush (from the previous game) and sprays Guybrush with root beer. This causes Guybrush to regain consciousness.
Guybrush returns to Scabb Island to have the local carpenter reinforce his broken oar. He plugs this oar into the tree and proceeds to climb to a treehouse, where he spots the seagull flying away from a huge pile of different map pieces it had stolen. Guybrush has no way to identify the correct map piece, so he returns to Marley's mansion and grabs her dog. He throws the dog into the pile of maps, and the dog pulls out Marley's map piece for him, netting him the third map piece.
Spotting a telescope in a treehouse, Guybrush takes it back to Rum Rogers's hut, where he places the telescope in the hand of a large gorilla statue in the front yard. This causes a ray of light to shine into the hut directly at the correct brick in the wall. Guybrush pushes this brick, which opens the chute and takes him to the secret room where the skeleton of Rum Rogers Sr. sits in a bath holding the fourth and final map piece.
With all four pieces in hand, Guybrush returns to Scabb Island to get the maps combined together by expert cartographer Wally. While he works on the maps, Wally asks Guybrush to run over to the Voodoo Lady's hut to get him some love potion he had ordered. When Guybrush gets back to the cartographer's, he discovers that Wally and the maps had been kidnapped by LeChuck. Fortunately, Guybrush finds a large crate near the swamp that is addressed to be delivered to LeChuck's fortress, so he climbs inside. Two deliverymen appear, and take the crate away.
Tropes:
- Cruelty Is the Only Option: To steal the key to the crypt where Rapp Scallion is buried, Guybrush has to lock Stan in one of his own coffins.
- Dragged into Drag: The costume that comes with Guybrush's invitation to the party on Booty Island turns out to be a lavender dress.
- Fat Bastard: The governor of Phatt Island is obese to the point of being bed-bound, and is rather ruthless in trying to collect a bounty on Guybrush's head.
- Frame-Up: In order to get the near-grog from Kate Capsize, Guybrush has to slap her picture from one of her flyers onto his wanted poster, causing one of the guards to arrest her instead.
- Gargle Blaster: Rum Rogers Jr. brews extra-potent grog for drinking contests. With twice the calories and twice the alcohol of regular grog, it's so strong even he has trouble keeping conscious after one glass of the stuff.
- Ghost Amnesia: Guybrush temporarily brings Rapp Scallion back to life in order to get his piece of the treasure map, but Rapp briefly seems unaware that he actually died.
- List of Transgressions: Guybrush's "Wanted!" Poster on Phatt Island lists all the crimes he's committed during the game, and keeps getting amended the further in the game you go to the point of being an Overly Long Gag.
- New Jobs As The Plot Demands: Stan of Stan's Previously-Owned Vessels in the previous game now runs a funeral home on Booty Island.
- Noodle Incident: We don't find out what happened, but apparently between this game and the previous one Elaine and Guybrush had a nasty break-up.
- Open Mouth, Insert Foot: Guybrush sweet-talks Elaine into forgiving him, but immediately blows it by asking about her grandfather's piece of the map to Big Whoop.
