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Very complicated.

But basically, it builds on the continuity of the shows and movies, with some elements of past comic books and video games as well. The novels include many adventures that take place in between episodes of the shows, but also many stories that continue the saga after its end. See Star Trek: Destiny for an example of the latter.

The novels all try to be consistent with each other and reference each other. However, some sources, such as Star Trek Online for example, are inconsistant with the novels (although STO does draw heavily from the novels' continuity, it doesn't incorporate events from the newest novels).

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