The captain first appears in The Holy City level, walking through the streets with other pirates and wielding a sword. The sword glows (blue) like a hero weapon, since it is the sword used by Heinrich Kleemann. Despite appearing in the cutscene, the captain is not there when the game resumes, making him unfightable.
He later watches as the surviving pirates load the hostages onto their ship, and leaves on a boat with a Pirate Spearman just as the heroes reach the harbour.
He makes an ingame appearance in The Water Temple, leading a group of surviving pirates against the three heroes agter they destroyed the Pirate Stronghold in Pirates and Hostages. He is presumably killed by the Taslow Towers, along with all the pirates with him. Oddly, he is only level two here, but still retains his unique model.
The captain also makes an ingame appearance in A Cold Day in Hell. If the player chooses not to go through the ice pike valley, they will encounter him and a group of Ninjas, though he is treated as a regular Samurai. Oddly, he can be killed here, despite the level taking place before The Holy City.