The pirate story is a parallel for the lives of everybody in the comic. It reflects aspects of the minor characters and has moments of similarity with actions that Ozymandias performs (remember right at the end where Ozy tells Jon that he dreams about swimming towards a black ship?- that's also the last image in the pirate story), but its main link to the story is thematic.
The pirate story talks about doing evil while seeking a greater good. That's Ozymandias all over, and it is also reflected in the actions of Rorschach and the other "vigilantes".
/English teacher and major Watchmen fan
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