The keel for the current Yorktown was originally laid down in late-2384 at Copernicus Ship Yards. Construction on the Yorktown completed in mid-2385 and a month later the first shakedown cruise was commenced under the command of project leader Commander Lefler. The standard shakedown cruise was completed successfully and the Yorktown was ready to receive a full crew to begin standard operations in December of 2385. Finally, in February of 2386, Captain Trevor Hall, station commander of Deep Space Twelve, and his command staff were chosen to take up command of the brand new Century-class starship. A new staff was carefully chosen to take their place on Deep Space Twelve, and once in place, the captain and his crew were brought back to Earth to take up residence on the Yorktown. It was believed that the captain's experience, knowledge, and unique command style would be better put to use on the frontier than sitting on a starbase in the fringes. Captain Hall and his staff arrived on the Yorktown in March of 2386.
Their first mission was to infiltrate Klingon space and stop the actions of an alliance of growing Klingon Houses. Although a direct violation of the prime directive, both the Klingon High Council and the Federation Council jointly approved of the mission seeing that the disgruntled faction of the Klingon Empire, while small, could be a tipping point in the Empire capable of starting either a small civil war or problems with the Federation. These were two scenarios which neither the Federation nor the Klingons wanted to deal with. Moreover, the Klingon Houses seemed to be aided by a Federation war hero from the Dominion War: Rear Admiral James Sullivan. Jaded and disenfranchised by the Federation, and felt overlooked by Starfleet for promotion after his work during the war, Admiral Sullivan decided to take to the Klingon Empire where he easily fit in with a Klingon-like personalty. This was something that the Federation simply would not stand for.
Following the apprehension of Admiral Sullivan and his handover to the custody of Starfleet Security, the Yorktown was given orders to set course for the border of the Romulan Neutral Zone. From there the Yorktown began a six-month exploratory tour of duty heading along the Neutral Zone towards the Delta Quadrant. During the tour the Yorktown was able to explore twenty-six different star systems and a dozen other various phenomena. The Yorktown then received orders to report to Cestus III to deliver supplemental relief supplies following the abandonment of the Gorn Hegemony occupation of the planet.
Once the mission to Cestus III was complete, the Yorktown was ordered to report to Romulan space, in the aftermath of the Hobus Incident, to bring relief supplies to Romulan worlds. Following the exchange, the Yorktown met up with the starships Valkyrie and Hathaway and the task group headed to Rator III to assist the Romulan people in the establishment of emergency shelters and to set up industrial replicators. After dropping off Reman refugees at Rator III, the Yorktown's task group was then confronted into a standoff with a Romulan Tal'Shiar warbird wing led by the Chairwoman of the Tal'Shiar, General Sonara T'Daran. With the assistance of Admiral Tolak tr'Servek and the Romulan Star Navy, the Yorktown was able to save itself from combat and gather valuable intelligence from Admiral Tolak in return for the assistance the Federation was providing.
The Yorktown returned to Starbase 11 for a classified meeting on the status of Starfleet in the wake of the Hobus disaster. Without any time to waste, the Yorktown was immediately sent back out on assignment to rendezvous with the Klingon warship Ba'pok to discuss the terms of a possible non-aggression pact, or at least a cease-fire, on the recent aggression of the Klingon military against the weakened Romulan Star Empire. Using the opportunity and guise of the friendly terms between the Klingon Empire and Federation, a wing of Klingon Bird's of Prey attacked both the Yorktown and Ba'pok, severely damaging both before being fended off.
The Yorktown then returned to its exploratory duties where it remained until 2389, when Captain Hall was reassigned and his first officer, Elizabeth Ashcroft, took command. From there the Yorktown was reassigned to deep space exploration duties in the Delta Quadrant, removing it from 3 years of assignment near Romulan space.