On Cadomai Prime, the rogue Sith Darth Wredd assassinates an undercover Snivvian One Sith infiltrator. This is part of Wredd's one–man insurgency against the One Sith order. News of the assassination reaches the Galactic Empress Marasiah Fel on Coruscant who decides to take no action against Wredd since she deduces that he is "helping" the Galactic Federation Triumvirate by eradicating the One Sith order. Meanwhile, Ania Solo and her companions' freighter is picked up in space by the Pellaeon-class Star Destroyer Animus. The Empress was impressed with Ania's efforts at rescuing the Imperial Knight Yalta Val during the Carreras Incident. Ania and her companions are treated as guests by the Imperials. After receiving repairs to their freighter, Ania's companions AG-37 and the Mon Calamari Sauk depart into hyperspace.
Meanwhile, Master Yalta Val and his fellow Knight Jao Assam received orders to return to the galactic capital Coruscant for duty. While recuperating in a bacta tank, Assam received a Force vision of Darth Wredd killing Empress Fel. Disturbed by his vision, Assam confides in his Master Val who is skeptical of the threat posed by Darth Wredd. He reminds the younger Knight that hunting Darth Wredd is not their responsibility and that he has to remember to uphold his vows. Unable to make headway with Master Val, Jao Assam convinces his newly-found friend Ania to assist him in the hunt for the rogue Sith. They attempt to sneak off the Animus but are stopped by Master Val and a squad of Stormtroopers.
Master Val attempts to reason with the younger Imperial Knight, reminding him to obey his orders and to "trust that the Force would guide the Empress." Following a brief skirmish, Jao and Ania escape the Star Destroyer in a stolen shuttle. Their travels take them to the planet Nalyd, the homeworld of Darth Wredd's Nalydian henchman Dieben. Believing that Dieben holds the key to Wredd's whereabouts, the two companions decide to find him. While visiting an unidentified planet to transport a wild beast, Sauk and AG-37 learn about a resettlement operation on the poisoned planet of Dac, the homeworld of the Mon Calamari and Quarren species which was destroyed by a Sith bioweapon during the last stages of the Second Imperial Civil War. On Coruscant, Empress Fel learns of Ania and Jao's escape. She orders that the former be arrested and charges the latter with deserting the Imperial Knights, a crime which carries the death penalty.
On Nalyd, Jao and Ania discover that Dieben is about to be executed for various crimes. Before he can be executed, Jao and Ania kidnap him. During the escape attempt, Dieben is killed without divulging any information. Ania is able to defuse any tensions with the local authorities by exaggerating Jao's combat prowess as an Imperial Knight and convincing them to reach a peaceful settlement. From the Nalydian authorities, the pair learn that Dieben was heading to Dac. This leads them to speculate that the rogue Sith had taken refuge in the lawless Calamari system, which had become a base for pirates and outlaws in the wake of the Second Imperial Civil War. Upon arriving in the Dac system, they quickly discover that another rogue Sith Lord Darth Luft and his pirate associates had established a slaving operation in the Mon Calamari Orbital Shipyards. The pair also meet two slaves, Mon Calamari Aunt Luen and the Quarren Tikin, who reveal that Luft and his associates were luring Mon Calamari and Quarren refugees back to their ruined homeworld under the pretext of restoring life to Dac. Instead, the Mon Calamari and Quarren slaves were put to work building a pirate fleet.
Jao and Ania's party are then captured by Darth Luft who dumps them into an escape pod, which is jettisoned into the poisoned oceans of Dac. Prior to their capture however, Jao manages to get their Imperial communications droid to transmit a distress signal alerting the authorities about the existence of the pirate operation. Ania's associates Sauk and AG-37 intercept their transmission while in hyperspace. Traveling to Dac, they succeed in retrieving their escape pod from the ocean. After rescuing Jao and Ania, Sauk and AG-37 take their freighter to an abandoned shipyard above Dac.
Following their near–death experience, an argument breaks out between Jao and Ania over what to do next. While Jao advocates taking the fight to Darth Luft, Ania advises caution and urges them to wait for reinforcements. Unwilling to risk getting his son Tilin killed, the Quarren Tikin refused to have anything to do with his rescuers and returns to his captors. Unable to resolve their differences, Ania and her companions depart in AG-37's freighter while Jao heads off to confront the Sith. In an attempt to save his son Tilin, Tikin reveals the presence of the Imperial Knight to Darth Luft. However, the violent and sadistic Sith Lord callously murders Tikin. Unfortunately, the murder of Tilin triggers a slave uprising among both the Mon Calamari and Quarren. In the ensuing chaos, Jao Assam engages Darth Luft in a lightsaber duel.
Meanwhile, Master Val and the Galactic Alliance Navy Admiral Gar Stazi receive Jao's distress signal. Out of a moral conviction and despite the opposition of Empress Fel, Val and Stazi assembled a task force of warships, seatroopers and Imperial Knights to liberate the Mon Calamari Shipyards. Back in the Dac system, Ania and AG-37 are being pursued by pirate starfighters. However, the pirate ships are quickly destroyed by the Galactic Alliance task force, which exits hyperspace. The Galactic Alliance Navy's forces include the freighter Trand Cappa, which is used to flood the orbiting Mon Calamari shipyards, overwhelming the pirates and enabling the aquatic Mon Calamari and Quarren to gain the upper hand. Val then leads a boarding part of seatroopers and Imperial Knights who quickly disarm and apprehend the disoriented pirates.
Unwilling to go down in defeat, Darth Luft's pirates have one more trick up their sleeve. To ensure compliance from their Mon Calamari and Quarren captives, the pirates had kept their families as hostages. In a final act, the pirates expose these captives to zero gravity space. The breach is temporarily blocked by the formation of a large ice plum at the exit to the space door. Ania and her companions manage to save many Mon Calamari and Quarren lives by using their Imperial communications droid to active the door's controls. Following a prolonged duel in the flooded shipyards, Jao Assam succeeds in killing Darth Luft by impaling the latter with a lightsaber. With the defeat of the pirates, the liberated Mon Calamari and Quarren slaves are allowed to inhabit the flooded interiors of the Mon Calamari shipyards.
Following the Liberation of Mon Calamari Shipyards, Jao Assam reunites with Master Val. Despite knowing that the penalty for desertion is death, Jao refused to return to his duties as an Imperial Knight and to continue with his mission to hunt down Darth Wredd. Despite their differences, the two Imperial Knights depart on good terms. Jao and Ania continue their hunt for Darth Wredd. While travelling through hyperspace, Jao receives a transmission from Darth Wredd, who gloatingly informs Jao that he had been playing into the latter's hands by following his trail and killing Darth Luft. This brought the rogue Sith closer to completing his final plan. He even offered Jao a place in his new Sith Order, which would be based on the Rule of Two. Despite Jao's despondency, Ania assures him that he has done good by liberating slaves. If they could free slaves, she reasoned that they could also take down an "arrogant" Sith.