It sounds a little bit like The Sound of Music, which has a fairly large sub-story "The Rise of Nazism" alongside the main "Making of a Family" story. Maybe you could watch that film as well to get ideas of how to blend stories together.
It sounds like you might indeed have a sub-story, or second storyform, from your brief paragraph. Let's append '2' to everything for that sub-story... can you see that MC2 has a Resolve (Change or Steadfast)? Do you know who IC2 is? Can you see an emotional relationship between them that changes in some way?
From your description it sounds like the two storyforms might have a shared OS? Like this:
/ \ / \
RS1 OS_for_all RS2
\ / \ /
Or do you think there are two Overall Stories, each with their own Goal, Outcome etc.? That would look more like this:
/ \ / \
RS1 OS1 <-> OS2 RS2
\ / \ /
If this is the case, they might still have certain touch-points in common (stuff that does double-duty, e.g. "King abdicates the throne" might be Requirements in one story and Forewarnings in another), represented by the double-headed arrow pointing between them. But you should be able to summarize each OS separately in its own sentence or two. Like "the struggle to prevent the Duke's ascension" and "winning the hearts and minds of the pirate folk".
Also, for a sub-story, it's good if something about the sub-story's outcome impacts the main story in a major way. The obvious way to do this would be the sub-story's Goal could relate to the main story's Requirements, but there are plenty of other ways to do it probably. Hopefully you've already had some ideas along these lines.