With the 14th Rogue apprehended, the crews of the USS Halo and USS Voyager learn the disturbing truth: the stolen prototype starship is none other than the USS Protostar, a vessel equipped with experimental technology that makes it uniquely capable of high-speed travel and tactical superiority. Designed for advanced missions deep in uncharted space, the Protostar’s stolen capabilities now pose a serious threat in the hands of Section 31 operatives.

While Admiral Townsend and Commodore Janeway begin interrogating the captured 14th Rogue at Starfleet Command, their suspicions grow that Section 31’s ultimate plan involves using the Protostar’s advanced drive to access classified Starfleet locations or territories deep within enemy space. Worse, the ship's Protostar Drive could be weaponized to jump across Federation borders undetected.

The crews of the Halo and Voyager must now track down the Protostar, which is en route to an unknown destination. Paul Sleeford, the Halo’s First Officer, assembles a team to analyze the encrypted data left behind by the rogue agent, seeking clues to the Protostar’s next move. As they decrypt the data, it becomes clear that the ship is headed toward a strategically sensitive area near Romulan space, where Section 31 plans to provoke a conflict by posing as a Federation vessel on a secret mission.

With time running out, Janeway and Townsend lead a daring mission to intercept the Protostar before it crosses into Romulan territory. As they close in, they face the challenge of outmaneuvering the Protostar’s advanced drive systems and defensive capabilities. A thrilling chase ensues through deep space, with the Halo and Voyager working in tandem to disable the Protostar without causing a catastrophic incident.