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As a rule, Star Trek makes no effort to maintain continuity outside of its Live Action Television series and films -- in fact, for a while, there was a directive that tie-ins couldn't reference anything except the live-action canon. Novels, comics, video games, roleplaying games, technical manuals etc. draw from their common origins, but exist largely independent of each other save for occasional Shout-Outs or borrowed elements.
There is a modern line of Star Trek novels from Pocket Books which make an effort to be consistent in regards to continuity. Most novels from the year 2000 on are generally set within the same reality. This continuity is discussed on the Star Trek Novel Verse page.
Some of the older books have been retroactively absorbed into the "Novel Verse" continuity, most have not.
There are (naturally) many Star Trek comic books, including:
- Star Trek Starfleet Academy (Marvel series, 1996-1998)
- Star Trek Deep Space Nine: N-Vector (Wildstorm miniseries, 2000)
- Star Trek The Next Generation: The Gorn Crisis (Wildstorm hardcover, 2000)
- Star Trek Divided We Fall (Wildstorm miniseries, 2001)
- Star Trek: Year Four (2009). Chronicles the adventures of the USS Enterprise on the fourth year of the mission. Noticeably Darker and Edgier than the television series with Continuity Porn abounding.
- Star Trek Countdown (IDW miniseries, 2009: Billed as the "official prequel" to Star Trek and written by the screenwriters, it initially wasn't clear whether this is merely a part of the Expanded Universe, or canon in its own right. After being questioned on certain (minor) inconsistencies between the comic and the final version of the movie, the screenwriters declared it non-Canon. The later Star Trek: Picard series was the final step to officially de-canonize it, presenting an irreconcilably different take on Picard's involvement in trying to stop the Romulan supernova.
- Star Trek (IDW series 2010-2018) : A retelling of Original Series episodes based in the alternate timeline started by the 2009 film. Unlike most Star Trek EU works, the films' creative team did have some influence on the comics and attempts to maintain continuity between the films and the comics were made, to an unprecedented, if not total, degree of success and continuity.
- Assimilation² (IDW miniseries, 2012): Crossover miniseries with Doctor Who.
- Harlan Ellison's The City on the Edge of Forever (IDW miniseries, 2014-2015), a limited-run series based on the original draft of the iconic episode.
- The Primate Directive (IDW miniseries, 2015): Crossover miniseries with the original Planet of the Apes film.
- Mirror Broken (2017-2018), a semi-sequel to the Doctor Who crossover, this trilogy focuses on the Mirror Universe counterparts of the Enterprise-D crew, set some time in TNG's fourth season, as they try to plunder the lush Prime Reality.
- Star Trek vs. Transformers (IDW miniseries, 2019): Crossover miniseries with The Transformers.
- The Q Conflict (2019). Celebration crossover featuring the crews of Kirk, Picard, Sisko, and Janeway as pawns in Q's game.
- Star Trek: Year Five (2019-) Ongoing series chronicling the last year of the original Enterprise's five-year mission.