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Plot summary
The novel is divided into two storylines. In the first storyline, Grand Admiral Thrawn and Darth Vader travel to investigate a disturbance in the Force on the planet Batuu, which lies on the edge of the Unknown Regions. In the second storyline, Anakin Skywalker travels to Batuu after his secret wife Senator Padmé Amidala disappears while on a mission to investigate the disappearance of her handmaid Duja. Point of view characters include Thrawn, Skywalker, stormtrooper Commander Kimmund, and Imperial Navy Commander Karyn Faro.

Mission to Batuu
Sometime after the trial and exoneration of Ahsoka Tano, Senator Amidala briefs Skywalker about her upcoming trip to Batuu to meet with her handmaid Duja, who has discovered something of interest to the Galactic Republic. Skywalker is concerned about his wife putting herself in danger but Amidala is determined to come to the aid of her handmaid. Due to his commitments as a Jedi General, Skywalker is unable to accompany Amidala. Skywalker is later alarmed by reports that Padmé's ship has been found abandoned on Batuu.

An unlikely ally
Exiting hyperspace above Batuu, Skywalker and R2-D2's Eta-2 Actis-class light interceptor encounters an unidentified freighter. Following a conversation, the intruder introduces himself as Commander Mitth'raw'nuruodo, an officer of the Chiss Expansionary Defense Force. Thrawn seeks Skywalker's assistance in learning of the Clone Wars. Skywalker agrees to help in return for Thrawn's assistance in locating Amidala and Duja.

Skywalker finds Padmé's ship in small forest clearing thirty kilometers from Black Spire Outpost. Skywalker fights a group of smugglers upset at the presence of Amidala's ship in their landing spot. Commander Thrawn manages to break up the fight. Together, he, Skywalker, and R2-D2 investigate Amidala's ship. They find no sign of forced entry but find logs indicating that Duja's ship, a Nomad Four, had left a week before Amidala's arrival. The two make arrangements to travel to Black Spire to continue their search.

Skywalker and Thrawn visit a cantina in Black Spire where they ask the bartender about Padmé and Duja's whereabouts. The two are attacked by four assailants but subdue and kill their attackers. Thrawn deduces that the assailants had come to assassinate Skywalker and that a fifth companion is still at large. To track down the fifth companion, Skywalker come up with a plan to make it appear that one of the human assassins survive.

Thrawn and R2-D2 return to his Jedi starfighter with the body. While flying with the human assassin's body, an explosion in the Actis's portside repulsorlift causes it to descend rapidly. Skywalker manages to regain control of the ship and lands it among the trees. He is attacked by a droid assassin but Skywalker uses the Force to deflect the blaster bolt back at the droid, disabling it. Skywalker soon encounters Thrawn, who has captured the fifth assailant. The two search the assassin's Separatist freighter.

Padmé's mission
Earlier, Padmé sends a message to Skywalker as she lands on Batuu. After landing in Black Spire, she contacts Duja but hears nothing from her. After disembarking, Padmé asks a human man if he knows the whereabouts of someone named Kuseph Jovi, claiming that she had come to deliver his ship. The man directs her to a cantina in the middle of Black Spire.

Padmé travels to the cantina on her BARC speeder. In the town square, she finds Duja's body in an open coffin. Inspecting the body, Padmé deduces that Duja was murdered based on her battered face and stab wounds. At the cantina, Padmé asks the bartender about how Duja died. The bartender claims that Duja was killed in a speeder bike accident. Padmé then composes a song for the fallen Duja.

Padmé uses a concealed beckon call within Duja's brooch to summon her ship to a remote forest clearing. While checking the ship's communications systems, she finds out that Duja discovered a Separatist factory on Mokivj. Padmé decides to collect her belongings from her ship, send a message to Anakin, and then depart aboard Duja's ship, which is equipped with enhanced shields and heavy weaponry.

Jedi and Chiss
Returning to the present, Skywalker and Thrawn disable the droids guarding the freighter. They discover that the freighter was transporting alcoholic beverages and gold ingots. Thrawn deduces that the ship is transporting its goods to a Separatist manufacturing facility. They also find that crates are etched with an unfamiliar symbol. R2-D2 inspects the navigation computer and finds that the Separatist ship was traveling to Cermau.

Thrawn learns from the listening devices he has installed in the cantina that five individuals have entered the cantina and carried the unconscious bartender away. Thrawn explains that Chiss listening devices translate speech into powerful sonic signals which are processed by another device into a pattern of invisible flickering lights.

Returning to Black Spire in their landspeeder, Anakin and Thrawn are attacked by several thugs. The wounded Thrawn rams their landspeeder into their attackers. Following a fight, Anakin and Thrawn subdue the assailants. They question two prisoners including a cargo inspector named Oenti. One of the prisoners reveals that the bartender Janott has connections to the pro-Separatist Duke Solha.

Questioning their prisoners, Thrawn and Anakin determined that Padmé's handmaid Duja had discovered that the smugglers were using Batuu to smuggle supplies to a Separatist droid factor. Duja had entered a Separatist ship and contacted the Republic. However, Oenti's comrades had realized she was a spy. The smugglers had panicked and attempted to ship their gains offworld. However, before their ship had arrived, the landing space had been occupied by Ambassador Padmé's ship.

Oenti confirms that Padmé landed at Black Spire and wrote a poem for the deceased Duja. Janott and Oenti deny killing Duja, and Anakin confirms they are being truthful. When Thrawn announces that they are going to the Separatist base on Mokijv, Oenti, Janott and their companions attack Thrawn and Anakin. Anakin slays the assailants with the exception of Janott with his lightsaber. Janott confirms that Padmé survived and left in a different ship. Leaving the bar, Skywalker briefs Thrawn about the political dynamics of the Clone Wars.

Infiltrating Mokivj
Padmé travels on Duja's starship Possibility to Mokivj but her starship is intercepted and shot down by a Vulture droid. Padmé manages to crash-land her ship in a river. Padmé travels down the river in an escape pod and discovers evidence of a nearby mine and town. Reaching a bank, she encounters three local human men named LebJau, Huga, and Cimy.

Padmé bribes the men into not reporting her to Duke Solha and Separatist battle droids by offering them reward money; giving them a Corusca gem as first payment. From the men, Padmé learns that the nearby factory used to belong to the men until the Separatists took it over. Now, the men work as maintenance workers. LebJau reveals that the Separatist also took over a nearby mine. Due to the poor rations offered by the Separatists, the men had been fishing to cover their meager diet.

Continuing their search for Padmé, Anakin, Thrawn, and R2-D2 travel to Mokivj and infiltrate the Separatist factory, which also doubles as a Separatist base. Besides droid components, they also discover large quantities of a fibrous material. After a failed attempt to bluff the Separatist commander Duke Solha, Anakin and his companions are attacked by Separatist battle droids. Following a brief skirmish, Anakin and Thrawn are thrown into improvised cells. Thrawn devises an escape plan based on his observations of the base's layout. He also notices that battle droids are manufactured in the eastern wing of the factory.

Meanwhile, Padmé spends several days hiding inside LebJau's boat. Lebjau outfits her with a transponder wristband and clothes that allows her to infiltrate the Separatist factory. While navigating he way through the abandoned west wing of the factory, she witnesses Anakin, R2-D2 and Thrawn being captured by Duke Solha and his battle droids.

Behind enemy lines
In the factory, Padmé tries to enter a trapdoor but is stopped by Cimy and Huga, who warn her that she is putting herself in danger. She tries to convince them to give her another wristband only to learn that they cannot be transferred to other wearers. Meanwhile, Anakin and Thrawn used an improvised cord made from Thrawn's clothing to unlock their cell door from the inside.

Disguised as maintenance workers, Padmé, Cimy and Huga make their way to the detention block. Padmé uses her combat skills to take out two B1 battle droids guarding the door to the detention block. Before entering the detention block, Padmé promises to get LebJau, Cimy, and Huga their money. Inside the detention block, Padmé encounters Skywalker and Thrawn who have freed themselves. They come up with a plan which involves Padmé accompanying Thrawn to the factory's rooftop to retrieve Skywalker's lightsaber.

Padmé introduces Thrawn to Lebjau and informs him about their plan to destroy the Separatist factory. Though Lebjau doesn't want to lose his people's factory and jobs, he agrees to help them evacuate the workers. Padmé also informs Thrawn about Anakin's Marg Sabl lightsaber fighting style, which he learnt from his former Padawan Ahsoka Tano.

Meanwhile, Anakin chances upon Duke Solha in a section of the factory that produces B2 super battle droids whose armor is infused with a fibrous material. Duke Solha is testing a new type of Clone trooper armor with an unidentified man and woman. Skywalker tries to confuse Solha's droid sentries but that only alerts the Duke to his presence.

While navigating their way through the roof of the factory, Padmé and Thrawn manage to recover Skywalker's lightsaber. They witness several descending spheres which distract the Vulture sentries. Thrawn reveals that these spheres are part of a Chiss mission to steal a deflector shield generator from the Separatist factory. Padmé makes an impassioned plea for Thrawn to help them but Thrawn insists that his mission comes first.

A disturbance in the Force
Following the Battle of Atollon, Thrawn has earned the displeasure of the Emperor Palpatine for failing to capture the rebel group Phoenix Cell. Thrawn also disapproves of the Death Star project that the Emperor, Lord Vader, and Grand Moff Wilhuff Tarkin support; preferring instead his own TIE Defender project on Lothal. During a meeting with the Emperor and Vader, Thrawn advocates eliminating the rebel fugitives. However, the Emperor instead dispatches him and Vader to Batuu to investigate a disturbance he sensed through the Force.

A lengthy voyage
Aboard the Chimaera, Commander Kimmund of Vader's First Legion argues with Commander Karyn Faro about the berthing of his master's shuttle and the Darkhawk, a former Separatist freighter that has been repurposed for undercover operations. Kimmund and his stormtroopers also deal with Thrawn's Noghri Rukh, who has been trespassing the Darkhawk. Kimmund warns Rukh that he and his men are prepared to shoot him should he be caught trespassing again.

On the bridge of the Chimaera, Lord Vader convinces Thrawn and his crew to travel to Mokivj before heading to Batuu to save on travel time. Arriving at Mokivj hours later, they find that the planet has been devastated by an unknown catastrophe. Thrawn notices that the planet's moons are out of orbit and wants to investigate further, believing that this is linked to the disturbance on Batuu. However, Lord Vader insists on staying on track with their mission.

Return to Batuu
After a three-hour delay, the Chimaera arrives at Batuu. To avoid unsettling the locals, Thrawn and Darth Vader travel to the planet's surface in an unmarked freighter while the Chimaera remains in orbit at a safe distance. Despite Kimmund and Rukh's protests, Vader insists that he and Thrawn go alone. Flying over Black Spire, they find that the settlement has grown in size. After parking their ship, the two travel through Batuu. The town is home to several species including humans, Darshi, Shistavanens, and Jablogians.

Thrawn and Vader take an interest in the Darshi, a enigmatic alien species bordering the Unknown Regions. Thrawn learns from the local bartender Nodlia that the Darshi are recent arrivals who have disrupted trade on Batuu. Meanwhile, Commander Faro and sensor officer Senior Lieutenant Hammerly detect the arrival of several unidentified ships heading towards Thrawn and Vader's freighter. Faro alerts Thrawn and Vader.

At the Black Spire cantina, Thrawn and Vader are attacked by ten Darshi warriors. Thrawn realizes the aliens are speaking in a clicked code. Besides blasters, the Darshi deploy swarms of bio-engineered insects which transform into a sticky gray paste that traps their targets. Despite being pinned down, Vader uses the Force to turn the tables on his attackers, killing four of them with his lightsaber. During the attack, Vader also experiences the disturbance in the Force, which manifests in alien forms.

Meanwhile, Commander Kimmund leads a stormtrooper boarding party aboard the Darkhawk to board one of the unidentified alien freighters. The First Legion boarding party is assisted by Captain Vult Skerris of Defender Squadron One. Kimmund and his troops board the alien freighter but meet fierce resistance from the alien defenders. Kimmund also gets Skerris to blow out the ship's ventral cargo hatch in order to stop the aliens from destroying their ship.

A new threat
Following the skirmish at the cantina, Vader and Thrawn inspect a nearby clearing where two Darshi houses were cleared to make way for a freighter. Inspecting the third remaining house, Vader and Thrawn find ten cylinders used for unfamiliar purposes, which are brought back to the Chimaera.

Aboard the ship, Grand Admiral Thrawn, Commodore Faro, Commander Kimmund, and Captain Skerris discuss Kimmund's assault on the alien freighter. Kimmund expresses his objection to Rukh's presence aboard the Darkhawk during the engagement with the alien freighter. Thrawn orders his lieutenants to load the alien freighter in the sixth slot and to put the alien prisoners in the brig.

Vader and Thrawn return to Batuu to question Nodlia about the new alien threat. After showing knives recovered from the Darshi attackers, Thrawn questions Nodlia about the purpose of the cylinders. Nodia reveals that the unfamiliar aliens that the Imperials encountered are Grysks, an enigmatic alien species from the Unknown Regions who dominated the Darshi. While Vader is unfamiliar with the Grysks, Thrawn is familiar with the aliens, describing them as a nomadic alien species of terrifying warriors "who overwhelm their opponents through sheer numbers and ferocity." Nodia is afraid the Grysks will return but Thrawn reassures him they won't.

Returning to the Chimaera, Vader and Thrawn deduced that the Grysks hired the Darshi to set up a base and communications triad. The two also deduce that the cylinders are hibernation tanks. Under the Grysks' orders, the Darshi had brought the cylinders and their occupants to Baatu. Vader deduces that it was their sudden fear at the knowledge of what was to happen to them that triggered the Force disturbance that the Emperor felt. Vader and Thrawn decide to investigate the Grysks and their hibernating Force-sensitives.

Thrawn and Vader discuss the captured alien freighter with Captain Skerris and Commander Kimmund. Kimmund deduces that the freighter had come to Batuu for a pick-up and reports that the ship's entire computer system had been wiped clean. Thrawn deduces that the Grysks had evacuated their prisoners in a second freighter. Determined to investigate the Grysks, Thrawn orders Faro to set a course for a set of unknown coordinates.

Studying the enemy
During the journey, the Chimaera encounters a hyperlane disruption, caused by a gravity well projector and a cloaking device which the Grysks have laid in their path. Tensions emerge between Vader and Thrawn over the latter's secrecy regarding the Grysk prisoners and the mysterious Force disturbance, leading Vader to question Thrawn's loyalty to the Emperor. Thrawn's references to Anakin also grate Vader, who has sought to suppress any connections to his past. Despite their difference, Thrawn tries to convince Vader that the Grysks pose a threat to both the Empire and the Chiss Ascendancy.

At Thrawn's initiative, the Imperials set a trap for the Grysks using the captured Grysk freighter as bait. Two elliptical Grysk ships resembling Corona-class frigates take the bait. One of the frigates board the freighter. The Grysk boarders are ambushed by Lord Vader, Kimmund, and elements of the First Legion. Kimmund and his men manage to capture the Grysk frigate and seventeen prisoners. Under Thrawn's orders, the second frigate is destroyed.

While inspecting a Grysk set of armor, Thrawn discusses the art and history of the Grysks with Lord Vader. Thrawn informs Vader of the Emperor's interest in the Unknown Regions. Thrawn also orders Commodore Faro to bring the Chimaera to their location. He also gives her orders to place the new Grysk prisoners in the starboard ready block to prevent them from communicating with the earlier batch of Grysk prisoners.

In order to test the capabilities of their new adversaries, Thrawn and Vader allow their second batch of Grysk prisoners to escape their makeshift prison. The aliens attempt to seize the freighter Darkhawk but are intercepted by Commander Kimmund and his troops. Most of the Grysks warriors except four are killed. However, at least three of Imperial Hangar Master Xoxtin's crew members are also killed in the process.

Thrawn and Vader discover that the second batch of Grysk prisoners managed to contact their imprisoned comrades aboard the Chimaera through ultrasonic signals. They also find that the Grysk warriors have removed their teeth and replaced them with upper and lower moldings containing weapons components communicators, and lock-breakers. Thrawn also deduces that the Grysks are interested in the Darkhawk since they obtained the vessel from the former Separatist factory on Mokivj. Thrawn orders Faro to set a course for Mokivj while Vader decides to interrogate the surviving Grysks.

Rescue on Mokivj
While Thrawn commands the space battle with Grysk starships, Darth Vader leads the First Legion on an assault on the abandoned Separatist factory on Mokivj, which has been repurposed by the Grysks. Through the Force, Lord Vader senses eight Chiss being put into hibernation chambers inside the factory. Inside the factory, Kimmund and his men fight Grysk forces, who deploy unfamiliar technology including lightning guns and swarms of insects carrying immobilizing liquid stone. Vader uses his Force powers to help the Imperials gain the upper hand over the Grysks.

Kimmund and his men manage to rescue five of the Chiss prisoners, who turn out to be Force-sensitive girls. Meanwhile, the Chimaera and its starfighters engage the Grysk warships. Thrawn and Faro are aware of the Chiss prisoners. Faro realizes that the Grysk are concealing the three remaining Chiss prisoners among their warships. Under Thrawn's orders, Captain Skerris' Defender Squadron destroys the Grysk tugs. The surviving Grysk warships retreat into hyperspace. The Grysks also abandon one of Mokivj's errant moons, which they had been using as a base.

Secrets of the Chiss
After attending to the needs of the liberated Chiss prisoners, Thrawn meets with Lord Vader, who is angry that he has withheld information about Chiss Force sensitives. Thrawn explains that the Chiss use Force sensitive children to navigate through the dangerous Unknown Regions since they lack nav computers. Thrawn explains that Chiss Force sensitives are overwhelmingly female and eventually grow out of their Force powers as they reach adolescence and adulthood.

In order to rescue the three remaining children, Thrawn tries to convince a reluctant Vader to lend Imperial forces to finding the Grysk base and rescuing them. Vader reminds Thrawn of his oath of loyalty to the Emperor but Thrawn points out that the Grysks have already violated Imperial space by closing the Batuu hyperlane and attempting to move Mokivj's moons to block Imperial movement. When Vader reminds Thrawn of his failure on Atollon, Thrawn responds that his war with the rebels is not yet over and vows to defeat them.

In the end, Vader agrees to allow Thrawn to use Imperial forces to locate and attack the Grysk base and attempt to rescue the remaining children. However, he exacts a promise from Thrawn to pull back if the battle goes against them. In return, Thrawn solicits Vader's help in using his Force powers to locate the Grysk base. Thrawn tells Vader that the Cheunh word for Force-sensitive is Ozyly-esehembo, which translates into Galactic Basic as "Sky-walker." Honoring his side of the bargain, Vader uses the Force to locate the system the Grysk base is in.

Old plot summary
A place where Anakin Skywalker and Thrawn had met before at the end of the Clone Wars (19 BBY). It was when Anakin went looking for Padmé who didn't return from a mission that he met the Chiss warrior and teamed up with him to look for her. They discovered the Separatists had set up a base on Batuu to deliver goods to a Separatist factory on Mokivj. This is where Padmé went. On Mokivj, she ran into locals working at the factory as part of the maintenance crew. Anakin and Thrawn followed her tracks to Mokivj. They met Duke Solha who controlled the factory. The Duke captured Thrawn and Anakin. Padmé made it into the abandoned West wing of the factory and noticed Anakin when he and Thrawn were arrested by the Duke. Padmé came to their aid to find them just escaping from their cell. Chiss ships arrived to retrieve a shield generator which had been Thrawn's original mission. Thrawn, however, returned to help Anakin and Padmé. When Anakin fought the B2 super battle droids inside the factory his lightsaber switched off every time he hit them. Blaster shots were absorbed as well. They learned that the factory was using cortosis (which was mined across the river) to strengthen the battle droids' armor, making them indestructible against blasters and even lightsabers. They also learned that in another wing of the factory clone trooper armor was produced using the same technique. Anakin suspected the Separatists were planning to infiltrate the Republic Clone troops. Thrawn was more suspicious and later hinted at the factory producing for the Republic as well as the Separatists (planning to use the enhanced Clone Trooper armor for when Order 66 would be issued). Anakin destroyed the factory and planned to collapse the mine across the river as well. Thrawn and Padmé opposed and pleaded not to harm innocent civilians taking away their livelihood. When Anakin set the charges the cortosis magnified the impact and lava erupted all over the area destroying farmlands and poisoning soil and water for years to come.

In the now, Vader and Thrawn traveled on board the Chimaera to Batuu to check out a disturbance the Emperor had sensed. At its main settlement 'Black Spire' they learned of the Darshi who started gathering there half a year earlier. The Darshi attacked Thrawn and Vader who were able to defeat them. It turned out that the 'Grysk', a warlike species from the Unknown Regions, had used the Darshi to set up hibernation tanks. Those tanks were used for Force-sensitive Chiss children. The Chiss used those (mostly girls) with Force sensitivity to navigate their ships through hyperspace without nav computers. The Grysk, having learned about their secret were trying to replicate it. The children's fear caused the disturbance in the Force the Emperor had sensed. The Grysk were mortal enemies of the Chiss and Vader questioned Thrawn's loyalty. When the Chimaera left Batuu they were attacked by the Grysk. Thrawn observed them in combat and concluded that they possessed techniques they could have only learned on Mokivj. Thrawn also suggested that Vader and Anakin Skywalker were the same person which was denied by Vader (not fooling Thrawn who could see through the charade). Vader later realized that Thrawn indeed knew the truth. On Mokivj, Vader led the First Legion to rescue the Chiss children, managing to save all but two. The Grysk mothership escaped with the last two. Vader and Thrawn chased it further into the Unknown Regions. Catching up with the ships they were able to defeat them and free the last two Chiss children from captivity. After the battle, Thrawn suggested that the Grysk led the Separatists to Mokivj in the first place all those years ago as they observed the Clone Wars from a distance and studied first the Republic, then the Empire. He feared the Grysk would become a major threat to the Empire. He also acknowledged that the Chiss were on the verge of a civil war as some had aligned themselves with the Grysk. Vader realized that Thrawn's loyalty was first and foremost with the Chiss, but the Emperor obviously knew and would allow Thrawn to work under Imperial command as long as he was useful.