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It jumps forward to the 23rd century, to follow the parallel careers of Melissa Sturdevant and Nikolai Barstow, Starfleet officers with illustrious careers. Each one seems to be a lynchpin around a conspiracy at Starfleet Command; each has a mentor with a hidden agenda.
A series of vignettes:
- Senior officers of the USS Enterprise exchange places with their counterparts in the so-called Mirror universe during an ion-storm influenced transporter accident in 2268 (TOS: "Mirror, Mirror");
- 2284: The discovery -- by the officers and crew of the USS Tereshkova -- of a Slaver "stasis box" with an ancient prototype of a Romulan cloaking device. (Star Trek: Shadowstar Station: "Hegemony")
In 2287, a Starfleet admiral, Helena Pope, handpicks Starfleet officers for what she calls the "Strategic Hazards Division". She is cognizant of many at the Admiralty who are involved with Section 31 and tells their leadership that they will be left alone in exchange for their non-interference in an operation.
In mid-2288, officers from different divisions of Starfleet are selected to work for Operation Blackjack (so named for Sector 212121). Some are sent to the mirror universe to replace their counterparts there, never to return. Some remain in the prime universe to out those officers of the mirror universe who have infiltrated key posts within the Federation. Some of those outed -- and who commit suicide rather than give up their secrets -- are the counterparts of friends and family.
The Federation President, Ra-Ghoratreii, makes a difficult decision to reach out to the leadership in the Klingon Empire and the Romulan Star Empire, as the situation may pose a threat to all of their worlds. Overtures are also made to other starfaring governments.
Ultimately, the Federation starship Iblis is used to destroy a portal connecting the two universes. The cost is that many "prime" Starfleet officers are stuck over there and there still remains the possibility that some "mirror" agents are in the prime universe.
Despite the loss of 60% of the Starfleet personnel assigned to it, the operation is considered successful.