Philosophy of Star Trek:
Some people call Gene Roddenberry an athiest; some call him a humanist. The truth is far different and far more complicated and requires some thought and open-mindedness to understand.
Gene created Star Trek in an attempt to explain his ideas and to attempt to guide humanity toward the path he envisioned.
If you wish to create new Star Trek in the spirit of Gene Roddenberry, and to understand his message about humanity and the universe (and even his cosmic theology), please be familiar with the contents of the following works; and note that his version of Star Trek was very different from the versions of Rick Berman, Manny Coto, or CBS All Access (which has too many rotating show runners to be able to list them all here).
Gene talks with Spock
Gene's throughts about God vs. Religion
Infinite Diversity in Infinite Combinations
Although not written by Gene, the series of Spock Vs. Q conversations by Leonard Nimoy and John de Lancie are also helpful.
The wisdom of