Order 66: A Republic Commando Novel is the fourth novel of the Republic Commando Series written by Karen Traviss.
As the Clone Wars continue to rage across the galaxy, spreading the Jedi Order and the Grand Army of the Republic very thinly in the war against the Confederacy of Independent Systems, Kal Skirata and his adopted clone trooper sons of Omega Squad, Delta Squad and the Nulls, as well as Jedi Knight Etain Tur-Mukan, plan to defect to the planet Mandalore to live normal, civilian lives.
As Skirata continues to search for a cure for the clone troopers' accelerated aging process, things get complicated when Etain finally reveals to Darman that her son, Kad Skirata is also Darman's son. Darman feels betrayed at both Etain and Skirata for keeping Kad a secret from him, which leads to Darman beating Skirata badly as the clone's father-figure doesn't even retaliate to let Darman release his anger.
Meanwhile, Ordo marries Besany Wennen, whose spying into Republic files is finally gaining attention. The Gurlanins even frame one of Besany's friends, Jilka Zan Zentis, for the hackings to cover for Besany. Fortunately, Walon Vau, Ordo and Wad'e Tay'haai save Zentis after the three trick the prison guards at the prison Zentis is being held in, into believing they are transferring her out.
Bardan Jusik also plans to break out Dr. Ovolot Qail Uthan, captured by Omega Squad nearly three years earlier on Qiilura. Skirata and Mereel have managed to manipulate different groups of scientists to research certain cells in the clones' genes to give the clone troopers normal life spans, and they believe Uthan might be able to piece all this information together.
On Coruscant, Etain plans to leave the Jedi, even disregarding joining a more liberal group of Jedi that have decided to join the war in the mainstream Jedi Order's favor because she believes that would be having the best of both worlds and ignoring the issues that caused Bardan Jusik to leave the Order in the first place. Darman forgives both Etain and Skirata for keeping Kad a secret, and begins to spend time with Etain and his son. Things also become too dangerous for Skirata as he becomes a wanted fugitive by Supreme Chancellor Palpatine's orders for stealing the late Ko Sai's clone data. Atin also marries Laseema, who is looking after Kad for Etain while she was away on Coruscant.
Meanwhile, Skirata's son, Tor Skirata, contacts Kal and informs them that he and his brother, Ijaat, haven't heard from Skirata's daughter, Ruusaan (whom hasn't signed the Mandalorian divorce contract that separates parents and offspring legally), in several months. Skirata pieces together that Ruu has been captured as a prisoner of war by the Republic because she had been working for the Separatists. Fi Skirata, Spar, and Sull all act as prison authorities to free Ruusan, with Bardan acting as another prisoner who can identify Ruu. Afterward, Ruu was highly grateful to her father for having her freed and reunited with the family.
Darman and the rest of Omega, as well as Delta, begin to encounter clones who aren't as trained or coordinated in combat as they are, and even hear that Kamino doesn't even rain. This corresponds to the new information coming from Besany that Palpatine is making a batch of new clones on Centax 2 from Spaarti cylinders, which makes instant mature clones in less than a year with no accelerated aging afterward and Skirata's group begin to fear that these new less-trained clones might replace the truly trained Kamino clone. Skirata decides on a date to finally defect from the Republic and leave the Clone Wars - 1,090 days after the Battle of Geonosis.
Later, Etain leads the Mission to Kashyyyk with Delta Squad 1,080 days after the Battle of Geonosis. However, the mission ends in bitterness for Etain and Delta as Sev is lost and presumably killed, and Etain and Delta are pulled back by orders that came directly from Grand Master Yoda even as they all want to save Sev, especially Scorch who almost disregards the order completely and tries to go after Sev. Scorch's grief at Sev's loss furthers his anger from being a comedic character to a tragic hero, exemplified by his killing of Separatist terrorists at a Republic outpost because those terrorists bombed the building the clones were in, killing and wounding many clones in the blast.Separatists invade Coruscant where Omega Squad and thousands of other clones, including the newly bred from Centax 2, fight against the battle droid and droid starfighter forces unleashed on the planet's surface. The battle lasts for five days, where Skirata and his clone sons estimate that Palpatine's newly produced clones were for defense purposes for Coruscant when the Separatists finally invaded the Republic capital planet. They even manage to take advantage of the battle as a distraction to spring Uthan from prison, and they also free Arla Fett, Jango Fett's insane and lost sister. The battle finally ends when General Grievous defects from the battle to return to Utapau. Afterward, as Etain is pulled off Kashyyyk, she sends a message stating she is officially resigning from the Jedi Order and accepts Darman's marriage proposal by comm. But as Skirata's defection date grows near, Chancellor Palpatine utters the chilling words to clone troopers everywhere that is an order that cannot be denied: "Execute Order Sixty-six." All clone troopers must kill their Jedi commanders immediately.
Soon, the Jedi are hunted down and many are killed with few survivors, but most of those survivors would be hunted down and killed by the newly declared Galactic Empire. Palpatine would establish, with himself as Emperor. The Jedi Temple is attacked by several clone troopers, lead by Darth Vader, where many Jedi are killed and the Temple is burned. Arligan Zey, who escaped the raid on the Jedi Temple, although severely wounded, is found by Captain Maze shortly after Ordo enters Zey's office to erase incriminating evidence in the Republic mainframe so Skirata's group wouldn't be tailed by Palpatine's New Order. Zey explained Palpatine is a Sith Lord, which Maze didn't know until Ordo told him that the Sith was like the Jedi - only with the exact opposite views, but he retorts why the Jedi didn't sense Darth Sidious's dark side presence in the first place. Then, Zey ordered Maze to kill him and the captain, despite his reluctance, pulled the trigger.
Meanwhile, Etain, officially no longer a Jedi, secretly lands on Coruscant and disguises herself as an ordinary citizen on the planet while Skirata and the clones begin to search for her as the hour grows nearer for Skirata and the clones to depart to Mandalore. Etain is found by the group at a congested pedestrian traffic blocked off by clones to see if anyone on the bridge is a fugitive Jedi. The traffic erupts violently when the clones creating the blockage figure out that there are a group of Jedi in the crowd. The Jedi that have been figured out, except for Etain, defend themselves with their lightsabers and battle the clones. But Etain stands in the way of a random clone and one of the Jedi's lightsabers just as that Padawan would have killed the trooper. Etain immediately dies from her wound from the lightsaber strike, and Darman is left in shock just as Niner is wounded by one of the Jedi and his spine is broken, paralyzing him.
Skirata goes insane after Etain's death and Darman's shock and attacks the Jedi where the Jedi are all killed. Darman and Niner are both picked up by a medical LAAT/i and disappear as Jaller Obrim knocks Skirata out with a drug and take Etain's body away with the rest of Skirata's defecting group back to Mandalore.
With the exemption of Darman, Niner, Boss, Scorch, Fixer and Sev (still MIA back on Kashyyyk), the rest of Skirata's group finally settle down on Mandalore just as the Clone Wars finally end. Then Etain's funeral is held, with her cremation as Skirata adopts Etain posthumously as his daughter, and Skirata decides to save her ashes for Darman if they can ever find him. Walon Vau hints that he will be going to Kashyyyk to find Sev (stating he will be studying trees, which clearly isn't Vau), Arla Fett is slowly being nursed back to mental health and Dr. Uthan agrees to make up a cure for the clones' aging process. Later, Skirata decides to make a monument of all the clone troopers whom have died in the Clone Wars, and Etain is the only non-clone that will be represented in the monument.
One of the pilots whom Etain worked with back on her second mission on Qilura when she was secretly pregnant with Kad, Nyreen Vollen, comes to Skirata to state she has two Jedi - one of them who is nicknamed Scout and a Kaminoan Jedi. Skirata agrees to take them in.
On Coruscant, Darman, Niner, Boss, Scorch and Fixer's fates are all revealed - they have become Imperial Commandos for Palpatine's new empire, and Niner has been healed to fight again. Darman also puts his old self, the one who used to love Etain, his brothers and Skirata as a father, away for the new Imperial Commando Darman. The novel finally ends when the Empire comes to Mandalore to mark their domain.
Meanwhile, Fenn Shysa, a Mandalorian who tried to get Spar and Fi to claim Boba Fett's place as Mandalore and meet up with Palpatine's forces to discuss a deal. The very last scene of the novel shows Skirata calming Kad down since the baby is aware of the Imperial forces' intentions, reflecting upon how Skirata had calmed down Darman after the clone beat up Skirata for keeping Kad a secret from Dar and reflecting upon a scene fifty years before the Battle of Geonosis when Kal was Falin Mattran, a Kuat boy who recently lost his parents and was raised by a Mandalorian named Munin Skirata who calmed Kal down when he first took on the mantle of Kal Skirata to stop his nightmares of his parents' deaths.