Cortez was a skilled pirate captain that lived over a thousand years ago. Even after his death, his spirit (now reduced to a skeleton) was still bound to his massive hoard of treasure that he amassed in his life. He stole the Sapphire Star from the Koopa that was one of the four heroes that defeated the Shadow Queen a thousand years ago. Flavio's ancestors stole a valuable piece of his treasure, the Skull Gem, which was used to power his ghost ship. Mario and his friends journey with Flavio to Keelhaul Key to find the Crystal Star. Mario discovers Cortez's treasure and fights him, but since he is an immortal ghost, he cannot be destroyed. Since Mario was only interested in the Crystal Star, Cortez gladly parted with it (he says he never liked the Crystal Star anyways). When Lord Crump and his X-Nauts crew attacked the stranded sailors on Keelhaul Key, Flavio made a deal with Cortez: if he returned the Skull Gem that powered Cortez's ship, Cortez and his crew would help defeat the X-Nauts. Afterwards, he helps transport everyone back to Rogueport and allowed Mario and his companions to sail back and forth between Rogueport and Keelhaul Key.
Battle Tactics
Cortez is very strong in battle. In his first form, he attacks by stabbing Mario or his partner with one of his blades. He can do this once for large damage, or 4 times for 2 damage per hit. In this form and the next, his head is high above the battlefield and can only be attacked with Jumps, but he rests in the spiky Bone Pile. In his second form, he holds a gem in his chest, which can only be attacked after he attacks twice, although it has a defense of -3. He attacks by either charging up and firing bones, or headbutting Mario. In his third, true form, he hold his four blades next to him. These blades, the Cortez Blade, Cortez Rapier, Cortez Sword, and Cortez Sabre are enemies in their own right, and can be attacked, although they eventually return if defeated. Cortez himself attacks by biting Mario. After his HP reaches half, he inhales the souls of all audience members, recovering 1 HP for each member. It's best to use Flurrie in this fight as she is the most effective. Flurrie's Gale Force can completely rid away Cortez's weapons. Vivian is also recommended as Fiery Jinx can also disable the weapons. It must be noted Flurrie completely rids the weapons from the battle, whereas Vivian only disable's them for a couple turns.
With Power Lift influence Yoshi can be used for the fight as well. Though Flurrie and Vivian are the better options.