Two years after the events of Council of Blood, Kir Kanos is sought by a man named Ennix Devian, who is a threat to the galaxy large enough for Vima-Da-Boda to warn Jedi Master Luke Skywalker of Devian, the leader of a splinter faction of the Imperial Remnant known as the Restored Empire, wishes to reform the Empire under the ideals of Palpatine in the same vein as Kanos. To this end, Devian hires bounty hunter Boba Fett to retrieve Kanos, who was operating under his "Kenix Kil" pseudonym in the backwater region of Meenka, and bring him to the Restored Empire homebase of RZ7-6113-23. There, Kanos is acquainted with a massive army and fleet made up of Clone Wars-era hardware, which Devian plans to use to attack the homeworlds of both the Imperial Remnant and the New Republic and create a new order. Meanwhile, political turmoil erupts on various worlds due to the influence of Nom Anor, a man of unknown origin who arranges the theft of a small supply of the volatile and highly explosive material zinethium from a storehouse on Nyara.
Recognizing Devian as a corrupt "thug" and assassin with no moral value, Kanos rejects his political ideals, escaping from the base in a captured shuttle. He travels to Coruscant in an attempt to make amends with Mirith Sinn and warn her of Devian's imminent attack; however, he is unaware that the shuttle has been embedded with the zinethium stolen from Nyara, which is abandoned in orbit by Luke Skywalker just as it detonates. The blame falls on Kanos, who was accompanying Sinn to a possible peace treaty between the Imperial Remnant and the New Republic hosted by the D'Asta family. Soon after the attempted attack on Coruscant, the peace summit is disrupted by a squad of Devian's stormtroopers, and Feena D'Asta is killed in the ensuing firefight. With peace talks halted by what seemed to be a New Republic ambush, Admiral Gilad Pellaeon of the Imperial Remnant quickly launches a retaliatory fleet towards Coruscant; with the Imperial homeworld of Orinda left relatively undefended, Devian mobilizes his fleet to attack.
Amidst this political and military confusion, Kanos and Sinn make an alliance with Feena's father, Ragez, who offers his fleet to ambush Devian's fleet as it enters the Orinda system. They narrowly save Admiral Pellaeon from capture by Devian during the battle, and Kanos challenges Devian to a final duel. Kanos overcomes Devian and kills him, but is critically wounded in the process. He uses this opportunity to fake his death, allowing the New Republic to pardon him "posthumously" of his crimes while he recovered from his wounds in one of Ragez D'Asta's safehouses. D'Asta and his remaining daughter, the clone of Feena created by Black Sun which he adopted, help Kanos begin a new life, one without the Empire.
Crimson Empire III was originally planned for release in 2001 and later 2002, but the project was eventually shelved. The basic plot, set in the New Jedi Order era, was to have Kir Kanos fight Luke Skywalker, the last one left who was complicit in Palpatine's death. The concept of an Imperial Royal Guard fighting Skywalker was a concept Stradley developed for Marvel's Star Wars series, but was not allowed to use; it was the origin of the original Crimson Empire concept.
Besides Kanos and Skywalker, Mirith Sinn would certainly have appeared, and Nom Anor might have also. Besides the plot of Kanos fighting Skywalker, it might have provided an additional tie-in to the Bantam/Dark Horse invasion storyline. The short comic Hard Currency also seemed to be a prelude to Crimson Empire III.
In 2008, Mike Richardson announced that he and Stradley were working on the project again to finally wrap up the Crimson Empire saga. Several days later, however, Stradley announced that although there had been talks, the project was not going to happen. In 2010, at Celebration V, Crimson Empire III was announced for a 2011 release. Richardson and Stradley would be writing, with Paul Gulacy on the art. A prequel story titled The Third Time Pays for All was published in Dark Horse Presents #1 in April 2011. In July 2011, the solicit for the first issue was released, revealing the miniseries' subtitle as Empire Lost.