The Yorktown class continued to serve in the Federation Starfleet after its formation in 2161. They continued to serve well into the 23rd century. One Yorktown class battleship was assigned to a fleet just prior to the Omega Directive in 2272. The ship was destroyed alongside three other ships when dampeners shut down the fleet's shields. Then the defense grid vaporized the Yorktown class starship and the other ships in the fleet. The Yorktown class starship was captained by a man named Somerset.
No explanation is given for these vessels' FederationStarfleet-style registry numbers and their use of the "USS" name prefix, despite existing two years before the inception of the Federation.
The game software included numerous other names for ships of this class that were not prepared to be used in gameplay, and are hidden in the game's source code, including USS Aurbach, USS Boston, USS Commonwealth, USS Concord, USS Fenway, USS Liberty, USS Paul Revere. Possibly, these vessels were intended for some feature of the game that was not completed. For example, none of these ships are coded with registry number graphics like those the included ships possess.