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In 2368 the Endeavour was assigned to the Starfleet blockade fleet at the Klingon-Romulan border during the Klingon Civil War. It was the last ship to clear the drydock prior to the departure of the fleet from Starbase 234. During the initial deployment of the tachyon detection grid, the Endeavour was linked with the USS Ajax, USS Hood, USS Tian An Men, and USS Enterprise-D. (TNG: "Redemption II") Later that year, the ship was assigned to a patrol circuit in the Cleon system. (TNG: "The Game")
Captain Amasov of the Endeavour was involved in a conflict with the Borg sometime prior to 2371. After the encounter, Amasov reflected, "...It is my opinion that the Borg are as close to pure evil as any race we've ever encountered." (VOY: "Scorpion") In 2373, the Endeavour again faced the Borg at the Battle of Sector 001. (Star Trek: First Contact)
The Star Trek Encyclopedia (3rd ed., p. 604) further states that it is likely the engagement referred to in "Scorpion" was the Battle of Wolf 359, and that the Endeavour was the sole ship to survive the assault intact. However, there is no direct canonical evidence for this, aside from the fact that Janeway had to have been referring to an encounter that took place before Voyager was transported to the Delta Quadrant, and that one of the forty ships did survive the assault on the cube.
In a preliminary draft for Star Trek: First Contact, dated 29 September, 1995, an Endeavor was explicitly named as one of the starships engaged in the Battle of Sector 001 in scenes 10, "PICARD: Signal the Endeavor to fall back. We'll cover them.", and 11, "The Endeavor moves off as the Borg FIRE at the Enterprise and BLASTS the saucer section.".  These references did not make it into the final cut, though designer John Eaves was working on a preliminary design for the ship, albeit of an entirely different configuration. As he recalled, "In the early script there had been a ship called the Endeavour that used to play quite a big role. I was drawing that and the E at the same time. They were kind of similar shapes, so it was almost a way of trying things out. I thought, 'If I want to see this on the E, let me try it on the Endeavour sketches first.' I'd mess around with the body, tapering it to the nacelles in one sweepy part, things like that. It was definitely an idea platform for me. So, at this point I just put Enterprise on all the Endeavour sketches, because by that time Endeavour was gone and nobody had ever seen them!" (Star Trek: The Magazine Volume 3, Issue 11, pp. 48-49)