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, Starbase 6 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. Since it was the crew, and not the mechanical systems, of the ship that were targeted by the amoeba, it is likely that the Intrepid itself survived intact, although it is unknown whether or not the ship was salvaged by Starfleet. (TOS: "The Immunity Syndrome")
Background information Edit
The third edition of the Star Trek Encyclopedia described this vessel as a Constitution-class starship, with a registry of NCC-1631 (diagram, p. 212, or Starship Chart, p. 473) or NCC-1831 (Constitution-class entry, p. 85). 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 their 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 namelist 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 Intrepid, USS Hera and USS T'Kumbra also had a predominantly Vulcan crews. According the Star Trek Concordance by Bjo Trimble, the captain of 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 Enterprise receiving a distress call (which later turned out to be fake) from Intrepid, which by that point had been presumed destroyed for nearly five years.
Intrepid may have been named after any number of Royal Navy (HMS Intrepid) or US Navy (USS Intrepid, though the reference book The Making of Star Trek – pages 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 namelist in the summer of 1967) vessels which had borne the name. 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.