Imperial Commando: 501st is the fifth and last book in the Republic Commando series by Karen Traviss. Originally stated that there would be a sequel, the sequel was cancelled, due to intervening information with the animated Clone Wars series.
The book starts off three weeks after the end of the Clone Wars and the declaration of the new Galactic Empire under the new Emperor Palpatine's rule. Darman and his brother Niner, who has healed from his spinal injury on the night of Order 66, are now under the rule of Darth Vader's 501st Legion. The purpose of Vader's organization of clones, remaining loyal to the Empire after the Clone Wars, is to hunt down and kill any remaining Jedi, especially Jedi Masters and maybe Jedi Knights, but also to bring back Padawans for the Emperor's Hand to train as dark side users. Along with this Jedi-hunting objective is to hunt down for any Jedi sympathizers and clone stragglers whom have left Palpatine's rule, such as the clone members of Clan Skirata. Darman is having an inner struggle with himself as he tries to pull himself together from his wife Etain Tur-Mukan's death. Initially, the squad that Darman and Niner are recruited in incorporate two clones trained by Corellian Sergeants, Bry and Ennen, and Bry is killed in the first mission to Celen in hunting Jedi. Bry is soon replaced by a Spaarti-grown clone, Rede, and after Ennen terminates a thug suspected to be a Jedi, he commits suicide. Not looking for any replacements for Ennen, the squad decides to be a three-man deal, and Rede is granted respect by Darman and Niner when he single-handedly kills a Jedi named Borik Yelgo aboard a space station somewhere in the Outer Rim. Meanwhile, Darman and Niner are introduced to Roly Melusar, who gains great respect from the clones in the 501st Legion, including Darman and Niner, for his no-nonsense attitude, his deep sympathy for the clones as people and soldiers, and his deep hatred of Jedi and all Force-users in general, including members of the Emperor's Hand.
Meanwhile, on the planet Mandalore, Kal Skirat] sends most of his Null clone sons, Nyreen Vollen and Bardan Jusik, who Skirata just adopted as another son, to extract Darman and Niner from Coruscant Imperial Center. However, just as Darman and Niner head down to meet with Ordo Skirata, Mereel Skirata, Prudii Skirata, Jaing Skirata, Nyreen Vollen and Jusik, Darman has second thoughts as he thinks over that if one of the 501st Legion's purpose was to hunt down for members to be trained as a member of the Emperor's Hand, then his son Kad would be in danger. Seeing how he has the entire Clan Skirata watching over Kad, Darman decides to stay in the 501st Legion in order to monitor, and maybe even sabotage, certain activities within the Empire that might compromise Kad's safety. Being as one of Darman's closest brothers, Niner decides to stay, too, which brings Jusik, now recently adopted as one of Skirata's sons, Vollen and the Nulls back to Mandalore empty-handed. Nevertheless, Ordo has promised Niner to have comlinks installed both of his and Darman's helmets that allows them to communicate to Clan Skirata over on Mandalore. Jaing even manages to get some dirt on Melusar, and reveals that Melusar came from a planet that was erased from the Republic star charts because it was ruled over by a Sith cult that killed his father, thus triggering Melusar's hatred of all Force-users. This hatred of all Force-users, including all of the members in the Emperor's Hand who serve as intelligence for the Empire, allows Melusar to have Darman and Niner, as well as Rede, skim around Imperial Intel to handle out anti-Jedi operations without the Emperor's Hand's knowledge.
Skirata's plan to reverse the aging in his clone sons' DNA by Dr. Qail Uthan is compromised when Uthan's home planet of Gibad is attacked by the Empire because of their reluctance to join the Imperials. Most, if not all, of Gibad's citizens were exterminated by a FG36 toxin created by Uthan herself - a bitter irony - while the actual structures of the planet remain intact. Uthan decides to put a halt on the reverse-aging process for revenge on the Empire for what they've done to Gibad by developing another virus she plans to unleash to the Imperials on Imperial Center. Working with Mij Gilamar, who she has a budding romance with, Uthan receives the supplies she needs to create the virus from the clones, but first develops an antiviral that would render whoever would receive the antiviral immune to the virus Uthan is creating. Skirata, Gilamar, the clones and Jusik go into Keldabe to spread the antiviral around so that the citizens of Mandalore wouldn't be affected by Uthan's virus that she plans to unleash unto the Empire. During Clan Skirata's visit to Keldabe, they spot Dred Priest. Priest happens to be a hated Mandalorian, who is an avid member of the Death Watch, a Mandalorian society that wants Mandalore to return to its old imperial days. Priest was also part of the Cuy'val Dar, and on Kamino, he set up a fight club that clones had been involved in, where they were either brutally wounded or killed. For what Priest did on Kamino, Gilamar and Ordo lead Priest down into an underground chasm where Gilamar kills Priest by stabbing him in a vital artery in the leg. Priest dies from severe blood loss, and Gilamar and Ordo toss his corpse into a churning river.
Also as part of Skirata's plan to reverse the clones' accelerated aging, Ny Vollen ships in the ancient Kaminoan Jedi Kina Ha, who was engineered by the ancient Kaminoans to cheat death via old age. With Kina Ha is Esterhazy Tallisibeth Enwandung-Esterhazy], or Scout for short. Kina Ha's gracious and pleasant persona happens to almost change Skirata's view of Kaminoans, and Scout shows Skirata that the late Etain Tur-Mukan or Bardan Jusik weren't the only "sensible" Jedi he felt good to be around. Unfortunately, Clan Skirata comes to struggle with an inner turmoil over what would happen after Kina Ha's genetic material was used to reverse the clones' accelerated aging. Since the Empire is hunting down for Jedi, keeping Kina Ha and Scout for any longer than is needed would compromise Clan Skirata's safety. One alternative is to simply kill the two Jedi so they wouldn't reveal any information about Clan Skirata's location, willingly or otherwise, or they trade them off with maverick Jedi Master Djinn Altis. The Jedi problem merely gets worse for Skirata when Jusik and Vollen pick up renegade clone trooper Maze, and he has Master Arligan Zey with him, whom Ordo believed to be dead under Maze's hands on the night of Order 66. Zey figures out about Kad's nature, his Force abilities and his parents, and Zey finds out about the Jedi Order's flaws, such as how they are viewed as child stealers. Nevertheless, Skirata, against his better judgment and Vau's logic to simply kill the Jedi, decides to deal with Djinn Altis to trade the three Jedi, as well as wiping out their memories of Clan Skirata's location in case the Empire ever caught them and interrogated them about Skirata and his clanmates.
Darman realizes about the Jedi being under the same roof as Kad via Fi, and regrets his decision about not going with the Nulls, Jusik and Vollen back to Mandalore, believing Zey, Kina Ha and Scout a threat to Kad's well being as a free Mandalorian instead of an orthodox Jedi under Palpatine's rule. He also figures out about Skirata's deal with Djinn Altis, who is viewed as a threat to the Empire of reestablishing the Jedi Order, and Darman decides that he will hunt down and kill as many Jedi as possible, notably under Altis's rule, for Kad's sake, which would compromise Skirata's deal.