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The Clone Wars rage on. As insurgent Separatists fight furiously to wrest control of the galaxy from the Republic, Supreme Chancellor Palpatine cunningly manipulates both sides for his own sinister purposes.
Torrent Company’s Captain Rex agrees to temporarily relieve Anakin Skywalker of Ahsoka, his ubiquitous—and insatiably curious—Padawan, by bringing her along on a routine three-day shakedown cruise aboard Captain Gilad Pellaeon’s newly refitted assault ship. But the training run becomes an active—and dangerous—rescue mission when Republic undercover agent Hallena Devis goes missing in the middle of a Separatist invasion.
Dispatched to a distant world to aid a local dictator facing a revolution, Hallena finds herself surrounded by angry freedom fighters and questioning the Republic’s methods–and motives. Summoned to rescue the missing operative who is also his secret love, Pellaeon—sworn to protect the Republic over all—is torn between duty and desire. And Ahsoka, sent in with Rex and six untested clone troopers to extract Hallena, encounters a new and different Jedi philosophy, which shakes the foundation of her upbringing to the core. As danger and intrigue intensify, the loyalties and convictions of all involved will be tested. . . .
The novel mostly takes place on the planet JanFathal. Republic spy Hallena Devis acts as a factory worker on the planet, which is run by a fascist regime. The regime has allied with the Republic in order to counter the Confederacy of Independent Systems, to which the citizens of JanFathal wish to side on, since the Separatists are comparatively more democratic in their eyes compared to JanFathal's fascist regime and the Republic. Eventually, all electronic power to JanFathal is blacked out, and the Separatists attack the planet, resulting in the Battle of JanFathal.
Captain Gilad Pellaeon is on a shakedown cruise aboard his new Republic battle cruiser, and joining him is Captain Rex of Torrent Company and Ahsoka Tano, apprentice to Anakin Skywalker. They receive a distress signal from Hallena Devis on JanFathal for extraction, and joining Pellaeon's company is maverick Jedi Master Djinn Altis of the Altisian Jedi. Altis's allowance of his students to have romantic relationships and indulge in other actions deemed unacceptable by Master Yoda's Jedi Order causes an inner turmoil in Ahsoka's traditionally held beliefs that those who follow this path are destined to fall to the dark side of the Force. Nevertheless, Ahsoka joins Torrent Company, Altis and his two Jedi apprentices, Callista Masana and Geith Eris, both whom are romantically involved and engaged for marriage, down to JanFathal to save Hallena, whom Pellaeon is also romantically involved with.
Torrent Company, Ahsoka, Altis, Geith and Callista locate Hallena amid the chaos caused by the Battle of JanFathal inside a building. She is held by several factory workers whom Hallena has "worked" with. Hallena's captors are eliminated by her rescuers and they get back to the shuttle to which they traveled in from Pellaeon's battle cruiser, though Torrent Company loses one clone, Vere. However, while the shuttle is traveling back up to the cruiser, the latter ship is forced to go to hyperspace in order to avoid any further damage. The shuttle in which Hallena and her rescuers are traveling in know that they don't have enough oxygen supplied from the ship suitable enough to keep them alive long enough to get to the closest planet past JanFathal. Knowing they have no choice, they go back to JanFathal under cover. The Confederacy of Independent Systems has won hold over the planet with its fascist regime utterly destroyed and the Republic no longer on the planet's side.
Back on Coruscant, Anakin Skywalker gets a call from Captain Rex back on JanFathal, discussing their predicament on the captured planet. Anakin realizes that he needs to fulfill his duty to tend to his clone company and his apprentice, and leaves his secret wife, Padmé Amidala, for JanFathal. When he goes to the captured planet, he meets up with Torrent Company and Ahsoka, but also, consequently, Altis, Callista, Geith and their liberal Jedi views. Anakin, like Ahsoka, is conflicted with everything he was taught under Yoda and Obi-Wan Kenobi's tutelage, and also realizing that if he were trained under Altis, he could have been openly loving Padmé. Nevertheless, they all work together to get past the Separatist forces, stealing a shuttle from the enemy and race back for the space around JanFathal. And just as they're doing that, Captain Pellaeon's flagship returns to the planet's system and picks them up just as they are hunted down by Separatist starfighters. They successfully leave the system with one more casualty from the clone known as Ince. Anakin talks to Altis, who reveals that he was friends with the late Qui-Gon Jinn, who wasn't completely obedient to Yoda's Order to begin with either. It is hinted through the communication between Anakin and Altis that the latter is somewhat aware that Anakin has someone with whom he is infatuated with. Altis assures Anakin that the latter is always open to join with his sect, but Anakin decides to stay, seeing that since the mainstream Jedi Order is more associated with the Grand Army than Altis is, Anakin sticks by with the clones, even if it means sticking by Yoda's rules and the Republic's.
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