During the Yuuzhan Vong War, Wraith Squadron included Baljos Arnjak as one of its members. Possessing biological expertise, he was stationed at the Borleias garrison once the New Republic had taken control of the planet after Coruscant's defeat by the Yuuzhan Vong. Subsequently, he took part in the defense of Borleias to prevent the Yuuzhan Vong from retaking it. Later, he was assigned to accompany an intelligence-gathering mission to Coruscant, along with several Jedi.
While situated on Coruscant, Arnjak engaged in numerous scientific investigations of the Vongforming processes occurring on the world. Furthermore, he established communication with Coruscanti survivors. As the New Republic team readied itself to depart the planet, Arnjak emphatically declined to leave, asserting that his purpose in the conflict was to persist in studying Coruscant and to coordinate resistance initiatives among the remaining populace, with the goal of preparing for a future New Republic reclamation of the world. Years afterward, when the freshly restructured Galactic Federation of Free Alliances arrived to reclaim the planet, Arnjak was present to greet their forces with groups of partisans and resistance fighters.

Arnjak was a member of the New Republic Intelligence Service unit Wraith Squadron throughout the Yuuzhan Vong War, and he served as the unit's resident biological expert, specializing in Yuuzhan Vong technology. Before Coruscant's fall, Arnjak was instrumental in creating various tools that enabled the Wraiths to function within Yuuzhan Vong territory. These tools included ooglith masquer creatures that, when worn, allowed the Wraiths to appear as Yuuzhan Vong.
Following the loss of Coruscant to the invaders in 27 ABY, Arnjak and his fellow Wraiths proceeded to the New Republic garrison located on Borleias. This world had been seized by the Yuuzhan Vong prior to their invasion of Coruscant but was subsequently retaken by New Republic forces shortly after Coruscant's fall. The garrison was under siege by Yuuzhan Vong forces, who were determined to regain control of the planet. However, shortly after their arrival, he, Wraith Leader Garik Loran, and fellow Wraiths Elassar Targon, Bhindi Drayson, and Kell Tainer were assigned to accompany several Jedi and scientist Danni Quee on a covert mission to occupied Coruscant. A portion of their mission involved establishing resistance cells on the fallen world, while the Jedi joined them to investigate a dark side presence they had detected. For the mission, Arnjak provided the team with disguises, tizowyrms to interpret spoken Yuuzhan Vong, and miniature surveillance droids disguised as fungi.
The Wraith operatives, Quee, and the three Jedi—Luke Skywalker, Mara Jade Skywalker, and Tahiri Veila—were deployed onto Coruscant's surface through an orbital drop from the freighter Record Time. They utilized insertion pods disguised as debris and coralskipper husks. Upon landing on the planet, they discovered that the Yuuzhan Vong had already initiated the Vongforming process to transform the world's ecosystem, in addition to extensively looting the cityscape.
The group explored the world for a period, during which Arnjak and Quee conducted scientific observations of Coruscant's altered biosphere. When the group encountered a contingent of Yuuzhan Vong warriors, Arnjak and the others successfully masqueraded as Yuuzhan Vong. However, the other group of warriors challenged their right to be present. A conflict ensued, and Arnjak aided the Jedi in guiding the majority of the Yuuzhan Vong onto a precarious bridge, killing some of them. Subsequently, demolitions expert Kell Tainer destroyed the bridge and eliminated the remaining Yuuzhan Vong with an explosive device, ensuring their presence on Coruscant remained concealed as they continued their exploration.
As the infiltration team discovered a concealed facility within the multitude of devastated buildings they explored, Arnjak and Quee analyzed the room and determined that, in contrast to the majority of Coruscant's atmosphere, the room contained a higher concentration of oxygen and lacked the levels of world-altering toxins and carbon dioxide introduced into Coruscant's atmosphere by the Yuuzhan Vong. This facilitated easier breathing for the party, and they decided to investigate further. Skywalker uncovered the source of the cleaner air—a devourer tank filled with an organism that actively purified the air—but believed something was underneath it. After using the Force to prevent the organism within the tank from attacking him, he managed to uncover a hidden laboratory, which Arnjak and the others then entered, after Mara Jade Skywalker bypassed the defensive system using an Imperial-era password.
Within the room, Arnjak detected indications of violence—specifically, the Wraith discovered a decomposed Human female corpse, killed by a lightsaber. He also located an oversized Imperial suspended animation chamber, which he deduced had contained some form of test subject before it escaped and killed the woman. However, the laboratory was deserted, possessed functional power systems, and was isolated and defensible, making it their new hideout. In the meantime, they resolved to gather more information about Coruscant's condition and the nature of the facility to determine their next course of action.
The pause in movement allowed Arnjak and Quee to organize their readings and summarize their findings: Coruscant's orbit had been altered, bringing it closer to its sun and causing an increase in temperature. Also, the Vongforming plants that the Yuuzhan Vong had introduced were dying off, though Arnjak was unable to rationalize why. However, the scientists concluded that Coruscant's environment had been significantly and permanently altered by the Yuuzhan Vong occupation. As such, they recommended to Luke Skywalker that any contact with survivors on Coruscant be focused on helping the natives survive and evade the Yuuzhan Vong. Skywalker was initially reluctant to agree with that assessment, but eventually recognized its veracity and agreed, even though it meant admitting that the New Republic would not retake Coruscant for years.
Following that period, Arnjak and Quee continued to conduct scientific measurements of the planet from the hidden laboratory. However, along with Bhindi Drayson, Arnjak was also able to determine the nature of the test subject that had originally been held in the laboratory. As it turned out, the subject was a Force-sensitive Human named Irek Ismaren, who had been subjected to numerous biological and cybernetic alterations to turn him into a powerful Dark Jedi. However, a disturbance, which Arnjak surmised to be a groundquake caused by the Yuuzhan Vong invasion, caused Ismaren to emerge from his suspended animation chamber prematurely. As such, the Dark Jedi was little more than a killing machine, according to Arnjak and Drayson, as the higher levels of thought and memory had yet to be restored to him—he had killed his own mother, the female corpse they had found. Skywalker and the other Jedi, after receiving this report, began a prolonged mission to hunt down Ismaren, who now styled himself Lord Nyax. While pursuing the deranged Dark Jedi, two of the Wraiths found a serviceable transport sporting a hyperdrive, and Skywalker ordered an end to the infiltration mission—once Nyax was defeated, they would leave Coruscant. However, although the original plan had called for Drayson to remain on Coruscant to organize survivor cells, Loran had decided against implementing that part of the mission. Instead, Arnjak insisted that he remain behind to continue his studies. Somewhat reluctantly, Loran agreed.
While stationed on Coruscant, Arnjak gathered information from his camouflaged surveillance droids and provided the New Republic, which was later reorganized into the Galactic Federation of Free Alliances, with intelligence for almost two years. During this time, he reported the return of the heretic Shamed One cult leader Yu'shaa, who had led an uprising against the ruling Yuuzhan Vong castes. Arnjak managed to establish communication with some of these Shamed Ones, teaching them some Galactic Basic and cultivating a friendship with them in anticipation of a future Galactic Alliance invasion of the world. Arnjak also coordinated the resistance on Coruscant and maintained contact with Loran to keep him informed of events on the occupied planet.
When the Galactic Alliance launched its invasion, Arnjak was present to greet the landing forces and was reunited with his Wraith Squadron companions Tainer and Loran. He then assisted in leading the combined Shamed One and Galactic Alliance forces in an assault on Supreme Overlord Shimrra's citadel, which was ultimately captured. As a consequence of the invasion of Coruscant, Shimrra was killed, and the Yuuzhan Vong fleet in orbit suffered significant losses before surrendering, marking the conclusion of a conflict considered the most devastating since the Galactic Civil War.
Arnjak, similar to many of the other Wraiths, possessed a humorous disposition and enjoyed engaging in verbal wordplay with those around him, a trait frequently encountered by the Jedi who accompanied the Wraiths on their mission to Coruscant. Nevertheless, he was also committed to his mission, dedicating long hours to taking readings and conducting tests in challenging conditions. He subsequently demonstrated equal determination in continuing his work, willingly remaining behind on a Yuuzhan Vong-controlled world for two years. Despite his military experience, Arnjak was not entirely desensitized to the horrors of war, and some of the sights he witnessed on Coruscant were sufficient to temper his typically lighthearted demeanor.
Arnjak spoke Galactic Basic with a distinct Coruscanti accent, or at least an accent that Luke Skywalker associated with either natives of Coruscant or those who aspired to reside on that world.
Baljos Arnjak was a proficient biologist, considered second only to Danni Quee in expertise regarding Yuuzhan Vong biots. He personally developed ooglith masquers and counterfeit vonduun crab armor, enabling the Coruscant infiltration team to operate under the guise of Yuuzhan Vong warriors for a period. He was also regarded as an authority on Yuuzhan Vong society, which proved invaluable during his time on Coruscant.
Baljós Árnyak serves as the official Hungarian title for "The Phantom Menace." (It translates literally to "Ominous Shadows.") Arnjak first appeared in the Enemy Lines duology, authored by Aaron Allston for The New Jedi Order book series as a member of Wraith Squadron, a unit also created by Allston in an earlier novel. Arnjak later featured in the final book of the New Jedi Order series, The New Jedi Order: The Unifying Force, by James Luceno.