After five years in drydock, the newly refurbished and recrewed USS Republic launches from the Utopia Planitia shipyards on Mars. Within hours of emerging from her berth, a priority one distress call is received from the Ambassador class starship, USS Zurich. The Republic's crew has little time for introductions before they find themselves in a race against time to rescue the survivors. In a search of the Zurich's logs to find out the source of a subspace shockwave that tore through the vessel, pieces of a very sobering puzzle fall into place as it is revealed that a new, previously unknown alien race has performed their first surgical strike on the Federation. As a breach in ethical protocol haunts the Republic's captain, and a complicated pregnancy grips her executive officer, a mysterious visitor from the future leaves behind an artifact that shifts the balance of power in a new war against another shapeshifter empire.

It is the day following the rescue of the doomed ship USS Zurich, and the Republic crew works to return their own vessel back to some semblance of normalcy. However, it is far from normal for the ship's executive officer as her complicated pregnancy takes a turn for the worst, and the only prescription that can save her child is a piece of technology used only once before on a Federation starship . . . by the Borg. As the medical ship McCoy makes a rendezvous with the Republic to offload the wounded Zurich crew, the Republic's captain chooses to violate Starfleet regulations and risk upgrading the ship with futuristic technology to survive a potentially devastating encounter with the shape shifting Kreltans. Unfortunately, the ultramodern improvements prove less than effective when the foreshadowed combat ensues, and as the battle-worn Republic is forced to make an emergency saucer separation to evacuate the innocent, the captain finds himself fighting an enemy with a forebodingly familiar manifestation.

In the wake of the successful destruction of the Kreltan Dreadnaught Indwelling, the Republic's stardrive section returns to Delphi Station for repairs and re-mating with the saucer section. Two weeks have passed as the vessel is repaired and re-crewed, but during that time, a new war with the Kreltan Confederacy expands to other areas of the Federation. With a new rotation of officers, the Republic is ordered to investigate and destroy a possible Kreltan base hidden on the surface of a distant Demon-Class planet. Upon arrival, an away team is dispatched to the surface before a cloaked enemy ship surprises the crew. A distress call is sent to the USS Firestorm for assistance while the landing party is recalled, and an attempt is made to infiltrate the attacking dreadnaught. Just prior to the debarkation of another away team, the Republic's captain is briefly incapacitated forcing the executive officer to hand over command of the infiltration team to the new tactical officer. The latter is a blessing in disguise as the infiltration mission backfires and the team is overrun and replaced with shape-shifting imposters. With her warp drive damaged, the Republic is forced yet again to separate the saucer section to evacuate the majority of her crew under the protection of the Firestorm. Unfortunately, the stardrive section itself falls into enemy hands forcing the captain and first officer to self-destruct that part of the Republic. As the stardrive crew escapes to the surface of the Demon-Class planet, the retreating saucer section falls under command of a Kreltan operative impersonating a senior bridge officer. The Republic's stardrive refugees make a last stand in their struggle to survive behind enemy lines as the saucer is misled to a star system where a fleet of Kreltan warships awaits their arrival.

With the Republic in drydock and undergoing a complete refit, the tired and battleworn crew are granted two weeks of shore leave to rest and recuperate. However, the captain is haunted by the ghosts of the recent Kreltan encounter, and in a rash moment where he questions his own leadership abilities, requests to be relieved of his command for an extended period of time. The senior staff returns from vacation to find their commander gone and removed from the duty roster, but in military tradition, spend little time grieving while preparing the ship for her eventual re-launch. As a new stardrive section is installed, and a new captain arrives to take command, the previous skipper of the Republic has a change of heart, and pleads with an admiral who has himself been misled regarding the recent Kreltan incursion into Federation space. Heads collide when the new and old commanding officers find themselves working for a high-brass official who makes the Republic his flagship. In the midst of this power struggle, the executive officer contracts a malady that defies traditional medical treatment and thrusts him into a journey of the mind leaving the yoke of a physical body behind on a biobed. With a 24 hour deadline, the chief engineer and newly arrived helmsman struggle to rescue their XO from the ethereal abyss as the new captain confines the medical staff to their quarters and a recent visitor from the future returns to set the record straight.

An old enemy of the Federation has risen to show it's scaly face after a hundred years of silence. The Gorns, a warrior race of bipedal carnivorous reptiles, have lived in a relative peace with humans in the Cestus system since the establishment of the Metron Treaty on stardate 3067. At that time, M'Geth, a prominent Gorn naval captain, engaged in life-or-death personal combat against the long dead Captain James Kirk of the Starship Enterprise, only to suffer a humiliating defeat without a drop of blood spilled. Bent on revenge, the aging saurian returns to the Cestus system to settle an old score ... with a fleet of warships. Starfleet, in a covert intelligence operation to observe military activity along the Gorn border, has inadvertently (or perhaps consciously) violated the treaty that has kept the century-long peace. The Republic is dispatched to the blockaded system as an olive branch with hopes to resolve the situation. Meanwhile, on the surface of Cestus Three, the swift reclamation of the human colony by the Gorns leads to chaos, suffering, and the rise of a resistance movement with direct family links to the Republic. The sky is suspended as the Republic's first officer attempts an evacuation operation while the captain disembarks on a deadly mission to face M'Geth in yet another duel to the death. Only this time, M'Geth uses any means necessary to ensure victory.

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.