Originally commissioned as an Excelsior II-class vessel in 2305, the USS Heisenberg, registry NCC-2401, was intended to perform long-range exploration. She was severely crippled in 2326 by high-energy missiles from a violently collapsing star; upon her return to starbase she was deemed uneconomical to repair and mothballed, as intact Excelsior-class spaceframes were at the time being retired from active service and given over to act as luxury cruisers for Starfleet admiralty while the more versatile and modern Ambassador-class spaceframe took over exploration and patrol duties.
In 2371 amidst the tense climate preceding the Dominion War Starfleet began to reassess its mothballed spaceframes to see if they could be repurposed for military activity. The Heisenberg was highlighted as a potential salvage if it was required that Starfleet field additional units than could be handled by the shipyards' ability to produce new starships from scratch; however, the war did not necessitate the exhumation of the wreck, and by 2387 she had fallen into a state of relative disuse, though as part of the preliminary salvage operation she had been partially restored to functioning efficiency.
In 2376, the USS Equinox NCC-7238 had destroyed the covert Borg resistance movement known as Unimatrix Zero, freeing all of the drones who had been on that interlink frequency from unity with the Borg and making away with a valuable Borg transwarp device which they used to return home. Some of the drones freed had been Starfleet officers, and they brought back with them their knowledge regarding Borg transwarp technology, which creates a metastable Einstein-Rosen bridge through which a ship travelling at high warp moves to traverse space far faster than can be achieved through warp alone. The Starfleet Corps of Engineers worked with these former drones, in particular May Moravec, to develop and integrate transwarp drive into a Starfleet ship; the USS Heisenberg was exhumed, extensively rebuilt and refitted as a new revision of the Excelsior-class to serve as this testbed.
In 2391 the rebuilt Excelsior III-class prototype USS Heisenberg was cleared for departure from spacedock for the first test of transwarp drive on board a Starfleet vessel since the failure of the USS Excelsior in 2285; she successfully engaged warp drive and passed into a transwarp conduit, monitored by the Galaxy-class USS Venture keeping pace alongside her. However, the Heisenberg did not exit the conduit at the destination where the USS Challenger was waiting.