As repercussions of the Cestus Three disaster ripple throughout the Federation, Starfleet is stymied as Fleet Admiral Morozov is assassinated, and rouge elements scramble to cover their tracks. The Republic, during an extended stopover at Starbase 39 Sierra, receives her replacement captain as the former commander is greeted by friends who bring his body home to rest. With her doctor returning to face his father in the wake of a family tragedy, the ship's command staff is put on trial for their role in the recent incident with the Gorn Hegemony. New senior officers report onboard as a celebrity arrives to protect the innocent and bring light to the shadows of injustice. Despite the support of powerful friends, the Republic's executive officer faces murder charges in a court that brings insurmountable evidence against him and his comrades.

A new captain takes command of Republic as she embarks on her first mission since the Cestus Three disaster. While the ship resumes normal operations, things are far from normal on the distant planet of Sigma Omicron Five, where mishaps and accidents plague a terraforming project that's falling further and further behind schedule. Republic is ordered to investigate, and as her chief helmsman expands into a leadership role by taking charge of an away mission, forces conspire against him and his comrades while a xenophobic race of non-humanoid aliens arrive to stake their claim. Mystery abounds as the new chief of operations is abducted, and an old high-brass foe backs the captain into a precarious corner. With all hell breaking loose on the surface of the planet, Republic finds herself trapped in orbit while a renegade starship stokes tensions and leads the Federation to the brink of war.

Following their mission at Sigma Omicron Five, the crew of the Republic have an abrupt change in their mission directives. No longer receiving her orders from the standard Starfleet hierarchy, the Republic is transferred into a low profile, civilian-run branch of Starfleet, and her new homeport turns out to be none other than Deep Space Nine in the Bajor sector. However, the crew has little time to adjust as an attempt is made on the counselors life, and Captain Roth orders a hasty departure from their new home to trap the perpatrator aboard. Meanwhile, the whereabouts of the new chief operations officer remain unknown as she finds herself at the mercy of a high-ranking officer who exposes the truth about her insidious origins. As Republic embarks on her next mission deep within the Gamma Quadrant, the now isolated crew is shaken to their core by the tragic deaths of several of her senior officers. Their hearts and minds wounded beyond comprehension, the tables are turned as a sinister operative from the Orion Syndicate is confronted, and a long-time member of the crew reveals a hidden secret with origins dating back to the original launching of the Republic.

Four months into their stellar cartography mission in the Gamma Quadrant, Republic is contacted by a race of beings originating from a previously uncharted planet in the heart of the Ash'aar Nebula. Its surface devastated by alien invasion and nuclear catastrophe, the lingering population suffers from a cybernetic plague that threatens to drive them all to extinction. Altering course, Republic comes to the aid of the dying world only to be spurned by the government and exiled from the solar system due to xenophobic fear of the Federation posing as conquerers. While the captain regretfully extracts the ship from the situation, Republic's chief medical officer and helmsman go against orders by risking their lives to bring a controversial cure back to the moribund plague victims. Pursuit is complicated by equipment malfunction, and compounded by a surprise attack on Republic by an old enemy of Starfleet, leaving the marooned rouge officers to face the deathly realities of a lawless wasteland and an infuriated despot.

After Starfleet considers listing her as missing and presumed destroyed, the damaged USS Republic returns to Federation space after a lengthy, half-year long mission in the Gamma Quadrant, reuniting with her homeport at Deep Space Nine. There, the crew find a heap of overdue messages, a bleary-eyed former crew mate waiting to deliver bad news, and a hostile political climate that may spell the end of their careers in Starfleet. Acting on ambiguous orders, ninety percent of the vessel's crew is reassigned, and the ship quickly embarks on another clandestine mission to a highly classified destination: the notorious Federation supermax prison station known as Ananke Alpha. There, the remaining crew come face-to-face with the bane of their helmsman's existence, and undergo a secretive tribunal intended to extend the scales of justice to beyond the borders of the Federation. Instead, the trial serves as a catalyst that sends ripples of chaos throughout the galaxy, brings Starfleet to it's knees, and crosses the threshold into a dark new reality for the entire human race.