Chapter 5

The fifth Crystal Star is located deep within a pirate's lair on the southern island of Keelhaul Key. To reach the island, with the help of Flavio and Admiral Bobbery, they sail to the island with some Toads and Lord Crump in disguise (known as "Four-Eyes"). On their way to the island, Mario and co. are attacked by Cortez's Embers, which shipwrecks them on Keelhaul Key. Later on, some of the crew members are attacked by more Embers, and Bobbery sacrifices himself to save them. Bobbery says he is close to death, and after giving him his last request, they found out that he was just asleep; after Mario wakes him, he joins Mario's party. With the aid of Bobbery and Flavio's Skull Gem, Mario and co. enter Pirate's Grotto. After solving some puzzles, and after gaining another ability from a Black Chest Demon, they finally reach the lair of Cortez. After a battle, Cortez gives Mario his Sapphire Star. Afterwards, Lord Crump abandons his disguise and tells Mario that he will continue attacking him with his ship's cannons, until he hands over the Crystal Star. With the help of Cortez's ship and Flavio's Skull Gem, they defeat the invading X-Nauts, along with their leader.

In the X-Naut base, TEC-XX wishes to gain access to a disk at Grodus's room, and asks Peach to help him. After making an invisibility potion, she helps him and he promises to analyze the data. Peach then sends another e-mail to Mario, informing him of this. Meanwhile, in Twilight Town, Bowser and Kammy Koopa run into Lord Crump. The three get into an argument, which escalates to an armed confrontation between the Koopa Troop and the X-Nauts. However, Bowser inadvertently ignites the Superbombomb, knocking out both armies.

Back at Keelhaul Key, Cortez ferries Mario and his teammates to Rogueport. Mario gets the e-mail from Peach, telling them about what TEC is analyzing. Mario and his team then reveal the next Crystal Star's location, and visit Prof. Frankly for information.