In 2267, the starship USS Enterprise was en route to Starbase 9 for resupply, when it encountered a previously-uncharted black star, which trapped the starship in its gravity well. The Enterprise was able to escape by utilizing full warp power in reverse, but the resulting whiplash effect propelled the ship into a time warp, through which the Enterprise traveled to the year 1969. (TOS: "Tomorrow is Yesterday")
In 2399, the location of Starbase 9 was labeled in a star chart that was in Fleet Admiral Kirsten Clancy's office at Starfleet Headquarters. The base was located in or near to Federation space. (PIC: "Maps and Legends")
In a deleted scene from TOS: "Catspaw", placed between the departure of the black cat and the arrival of Sylvia, DeSalle inquired to Uhura the "time elapse for a message to and from Starbase 9", which he learned was "almost ten solar days" from their location at Pyris VII. DeSalle then requested that all the appropriate log entries of the past solar day were relayed there. This fact was later referenced in the Star Trek Encyclopedia (4th ed., vol. 2, p. 316).
Issue 2 of the comic book Who's Who in Star Trek established the starbase as having been constructed sometime during the 22nd century, and located close to Sector 001, near the border of the Miaplacidan Alliance. The comic also stated the location was chosen due to the proximity of the nearby black star which provided an opportunity for scientific study, and the base consisted of both planetary and orbital facilities.
According to the comic book Star-Crossed, in the late-2250s, the USS Eagle docked at the Starbase 9 space station facility before embarking on a planetary survey of Caperna IV, during Commander James T. Kirk's first month as starship first officer.
Starbase 9 was referenced in the Pocket TNG novelization of Relics, in which the Enterprise was headed for shore leave at the starbase when Lieutenant Commander Montgomery Scott celebrated his birthday in the year 2267. Commander Tattinger was also assigned to the starbase at the time.
In the comic book The Quality of Mercy, Commodore Markessan was the commander in the mid-23rd century. He resided on the starbase's planetside facility with his family. In the early 2370s, Markessan's son, Tak Markessan, was involved in a tragic ground vehicle accident which cost the life of his girlfriend, Lorina. Grief-stricken, Tak left Starbase 9 shortly thereafter in a shuttlecraft, bound for the Miaplacidan Alliance.