There are many moments in this movie between the Pirate Captain and the Pirate with a Scarf that seem to suggest that their relationship may be a bit more than platonic.
- The way the Pirate with a Scarf looks at the Pirate Captain when the the Captain takes the wheel just as they are about to dock at Blood Island at the start of the movie
- In the Pirate Captain's cabin, there is a figurehead holding a cup with two toothbrushes in it at the entrance to the Captain's bathroom. Obviously one toothbrush belongs to the Pirate Captain, but who do you suppose the second one belongs to?
- The scene when the Pirate Captain asks the Pirate with a Scarf to make "nautical noises" to help him go to sleep. According to the director, Peter Lord, Gideon Defoe, the author of the original novels, who also wrote the screenplay for the film, originally wanted to have the two of them in bed together!
- Also, during the bathtub chase scene, there are shots where one can be sure that the Pirate Captain and the Pirate with a Scarf are actually holding onto each other!
- When the crew leave the Pirate Captain behind after finding out that he had sold Polly to Queen Victoria, the Pirate with a Scarf is the last one to walk away. It is immediately after he does so that the song, "I'm Not Crying" by Flight of the Conchords starts playing. This is appropriate because in the actual clip for the song, the guy starts singing this song immediately after his girlfriend breaks up with him!
- After defeating Queen Victoria, the Pirate with a Scarf hands the Pirate Captain his hat back, as a gesture of welcoming him back onto the ship. The Captain immediately responds to this by giving the Pirate with a Scarf a tight hug. The camera immediately cuts to the crew cheering, making it look almost as though the Pirate Captain and the Pirate with a Scarf are getting married. The fact that Pirate with a Scarf freezes for a moment before hugging The Pirate Captain back with a gentle smile really makes it feel like two lovers making up after a big fight.
- In the scene during the epilogue when the crew give the Pirate Captain the makeshift "Pirate of the Year" award, the Pirate Captain asks the Pirate with a Scarf if he is a woman disguised as a man. Considering after everything they had been through together, what possible reason could the Captain ask his first mate such a question?
- Peter Lord, the director of the movie, stated in the Tumblr page he created for the movie, in his character description for the Pirate with a Scarf, "If the Pirate Captain is the crew's flashy and unreliable dad, then the Pirate with a Scarf is their slightly put upon mum." Pretty self-explanatory, no?
- Even in the books, there are some pretty suggestive moments between those two. For example, in the third book, The Pirates! In an Adventure with Communists, when the Pirate Captain offers Karl Marx a cigar, Marx asks the Captain is they had been rolled in the dusky thighs of a native Cuban woman. The Pirate Captain regrettably confesses that they haven't, but then offers to roll them on the thighs of the Pirate with a Scarf, apparently because he's the closest thing they have, despite the fact that they now have Jennifer, a Victorian lady as a member of his crew. Sigh, excuses, excuses, excuses...