As someone who hasn't played Kotor (well, much), or read any books, or generally knows all that much about Star Wars, here's what I can elaborate on:
The story to the game has a lot of layers.
The first layer would be "side quests". These all have an over arching plot that take place on the planet, and even though they're "side quests", they all come together to form a beginning and an end, although a good portion of them can be taken interdependently, but also factor into the whole. For example, completing a secondary quest to, say, help some guy destroy a crane, will result in the final dialogue saying something like "We have secured this planet, thanks in no small part to you destroying a crane" or something like that.
The next layer would be your class quests. These form a good portion of your main story, and probably where the most intrigue comes from. It's very good, but each class is different and has their own story, and from what I've seen, this story ties into the next layer, but - at least at level 40 - aren't related to the games over all story, but are rather pieces of it.
Then there's the games over all story, that the previous layers all tie into. This is basically the tenuous piece between the republicans and imperials. The imperials are trying to start a war, I don't really know what the republicans are doing (having not played one), and that is the overarching story between the planets and class quests.
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