In 2267, the Intrepid was undergoing repairs in maintenance section 18 at Starbase 11. The base commander, Commodore Stone, rescheduled the Intrepid's repairs, upon giving the USS Enterprise "priority one" status on stardate 2947.3, after being damaged in an ion storm. (TOS: "Court Martial")
In 2268, the Intrepid worked in conjunction with Starbase 6, in conducting a mission to investigate the loss of contact with star system Gamma 7A in Sector 39J. While traversing that sector of space, the Intrepid encountered an unknown dark zone which was, unbeknownst at the time, slowly killing the ship's crew.
On stardate 4307.1, the Starbase 6 commander lost contact with the Intrepid. A rescue priority was issued to the Enterprise to investigate the loss of the Intrepid in an unknown dark zone. En route, Commander Spock telepathically sensed the crew of four hundred Vulcans die.
On stardate 4309.2, the Enterprise established that the phenomenon destroying the Intrepid and the Gamma 7A system was an incredibly huge but simple cellular being whose energies were totally destructive to all known life. The crew of the Enterprise destroyed the amoeba, which was determined to be nourishing itself for reproduction. (TOS: "The Immunity Syndrome")
The fourth edition of the Star Trek Encyclopedia described this vessel as a Constitution-class starship, with a registry of NCC-1631 (Intrepid, USS entry, vol. 1, p. 373; ship chart, vol. 2, p. 331) or NCC-1831 (Constitution-class entry, vol. 1, p. 158). A ship diagram of the Intrepid in the third edition of the Encyclopedia on p. 212 depicted the ship with the registry NCC-1631. The registry NCC-1831 was seen in the chart in "Court Martial". Unfortunately, the chart didn't provide names to the registries. Greg Jein also originally used "1631" in his influential "The Case of Jonathan Doe Starship" article. (See the "The Case of Jonathan Doe Starship" article for the full explanation.) The Star Fleet Technical Manual assigned NCC-1708 to the vessel. According to the Manual, this ship's successor was to be called USS Intrepid II NCC-1730 and to be Constitution-class.
Due to the crew count of 430 that the writers of The Original Series had mentioned in the dialogue for "The Immunity Syndrome", it was, at the time, a likely assumption they inferred the vessel to be Constitution-class, especially since Original Series Producers D.C. Fontana and Robert Justman had, at the start of second season of The Original Series, already included the ship in a definitive list of fourteen ships belonging to what they, at the time, still referred to as the "Starship-class". (The Making of Star Trek, p. 165) Yet, it should be noted that neither class, registry, nor appearance were canonically established prior to 2008, as the ship has never been visibly featured in the original series run. It was only for the 2008 remastered version of "Court Martial" that the ship, seen in orbit of Starbase 11 with the registry NCC-1631, was digitally retconned into the episode and that Michael Okuda, in his role as Visual Effects Producer, had Jein's registry number applied onto the ship, only then confirming all three items in canon.
On his name list suggestion memo of 9 August 1967, Justman made the annotation, "In addition, I think a name ought to be made up that would be of Vulcan origin." Jein had picked up on this clue and included an "USS Tashik-Sotra (NCC-1865)" in his article, the only name he had not derived from production sources. Justman's notion, however, was watered down in merely having Intrepid a crew that was almost entirely composed of Vulcans. Like the Intrepid, USS Hera and USS T'Kumbra also had predominantly Vulcan crews. According to the Star Trek Concordance by Bjo Trimble, the captain of the Intrepid was Satak. This reference, like that of the similarly referenced IKS Devisor, may have been acquired from an early draft of the script. The Worlds of the Federation by Shane Johnson refers to a captain of this vessel being named Spiak. The fact that no Vulcans are seen on Starbase 11 in "Court Martial" may be due to the fact that Vulcans do not believe in the concept of shore leave, as Spock described in "Shore Leave".
The Star Trek: Phase II episode "Deadlock" was set to open with the Enterprise receiving a distress call (which later turned out to be fake) from the Intrepid, which by that point had been presumed destroyed for nearly five years.
The Intrepid may have been named after any number of Royal Navy vessels which had borne the name (i.e., the HMS Intrepid) or US Navy (USS Intrepid), though the reference book The Making of Star Trek (pp. 164-165) made it very clear that the Original Series producers had the World War II aircraft carrier USS Intrepid (CV-11, Essex-class) in mind when they came up with their name list in the summer of 1967. The lunar module of NASA's Apollo 12 was also known as Intrepid. In all cases, the name signified a willingness to go in harm's way to accomplish a mission of great importance.
Several novels mentioned the second Constitution-class Intrepid, such as My Enemy, My Ally and Prime Directive (Pocket TOS). Prime Directive has the under-construction Intrepid's nacelles diverted to be attached as replacements on the Enterprise, and My Enemy, My Ally described Intrepid, under Captain Suvuk, as being slightly more advanced than the as yet un-refit Enterprise of that era. My Enemy, My Ally referred to Intrepid, named so for the ship destroyed by the giant amoeba, as NCC-1631 a number previously used in Greg Jein's original article and FASA manuals. FASA's Enterprise-class Intrepid had the registry NCC-1707 and would be in service around this time. It has been very likely that it had been this Intrepid that was slated to make an appearance in Star Trek IV: The Voyage Home, before its scene was deleted.
In James Blish's adaptation of "The Immunity Syndrome" for Star Trek 9, Kirk says of the Intrepid, "The crew of the Intrepid is Vulcan, isn't it Mr. Spock? I seem to remember the starship was made entirely Vulcan as a tribute to the skill of your people in arranging that truce with the Romulan Federation. It was an unusual honor." Given that Blish sometimes worked with scripts earlier than the shooting scripts, this may have been an early intended version of the Intrepid's backstory.
The novel Vulcan's Forge mentioned a ship in the 2290s named Intrepid II that was an Oberth-class scout ship under command of Captain Spock. After his resignation, he proposed Uhura to be its new captain.
The novel Desperate Hours sets out that both Spock and Michael Burnham considered joining the Intrepid due to its Vulcan crew complement; Burnham's application for a position there being outright rejected by its captain, despite her "culturally Vulcan" nature.