With her fellow Jedi, Rar was incarcerated on the Exquisite Death, as Yaght selected members of the strike team for torture sessions with one of the voxyn. Kore was tortured extensively; already suffering from the severe wound to her back and the puncture to her single lung, the Bith was supported by the Force Meld as best the Jedi could manage in their weakened state. Commander Yaght questioned Kore continually on the existence of the secret Jedi base, and when the other members of the strike team began to feel that it would be easier on the wounded Bith if she relinquished the name and location, Rar grew worried, able to see that Yaght's goal was not to break Kore's spirit, but the spirit of the strike team. When she communicated this fear to Jaina Solo, Rar was struck and rendered unconscious by her captors. Despite her wounds, Kore soon managed to bring about the death of the voxyn, and the Yuuzhan Vong commander became aware that the Jedi were too dangerous to be incarcerated for a long period of interrogation. The Exquisite Death traveled faster toward Myrkr.
Rar led the Jedi to a warren which housed Force-negating ysalamiri creatures, as well as the Jedi presences Solo had detected on the approach. Rar killed two warriors in the storming of the ysalamiri warren with her new silver-bladed lightsaber. She then watched, with fascination, as a Human woman held in bonds against the rear wall displayed her strength in the dark side of the Force, utilizing a web of Force energy to dice a Yuuzhan Vong shaper into bloody fragments. Rar freed the woman, who identified herself as Lomi Plo. When Plo sensed Alema Rar's internal turmoil and thirst for vengeance, she appealed to Rar's darker emotions; although Solo warned the Twi'lek against such uses of the Force, Rar ignored the team leader, rounding upon the young man and proclaiming that when he had witnessed what she had during the war, only then could he lecture her about the dark side. As Plo and the other Dark Jedi with her, a younger man known as Welk, pledged their allegiance and aid in destroying the voxyn, the strike team learned that a Yuuzhan Vong frigate in orbit over the worldship had deposited over a hundred warriors on the surface.
Jaina Solo, Rar, and the rest of Twin Suns Squadron, along with the rest of Antilles' forces, were unaware that the attack upon Duro was a ruse, as was a task force of Duros, who broke formation and continued the battle against orders. The Duros contingent of the Galactic Alliance fleet was wiped out, casting a pall over the victory celebrations, which Rar attended. In a cantina with her squadmates, Rar was present when a Duros, Lensi, who had flown with Rogue Squadron during the battle, confronted Solo and accused her of lying to the Duros about the objectives of the battle. Solo defused the situation, reminding Lensi that everyone had suffered losses during the war. Having originally intended to resign from the military, Lensi saw reason in Solo's arguments and remained with Rogue Squadron.
Without the leader of the Order, or knowledge of the whereabouts or status of the missing Jedi, a meeting was convened in the apartment of Master Tresina Lobi in Coral City's Quarren Tower. Rar attended alongside a group of whichever Jedi could be mustered, and Master Kenth Hamner addressed the assembled Knights and Masters on the issue of the Skywalkers and their companions. The group discussed the idea of inserting a strike team onto Coruscant to interrogate a mysterious figure, the Prophet Yu'shaa, who was leading a resistance movement against the Yuuzhan Vong rulers and was suspected to hold knowledge on the whereabouts of Zonama Sekot. The similarity of the plan to that of the Mission to Myrkr was obvious, as were the risks, and it was intended as a last resort; if Skywalker and his companions failed to make contact within a week, Hamner planned to assemble the strike team of Jedi, of which Rar would be a member.
With her first plan having failed, Rar attempted to isolate Solo from his wife so that she could carry out Plo's directives, to no avail. Further complications arose when the Millennium Falcon was obstructed in hyperspace by a nebula; usually, it was a simple method of disengaging the hyperdrive and avoiding the nebula, but Rar's sabotage ensured that this could not take place. The light freighter's destruction was soon imminent; fortunately for its occupants, Organa Solo spun the Millennium Falcon around in hyperspace and fired the sublight engines. Time and space were briefly distorted, before the freighter dropped out of hyperspace, dragged out by the mass shadow of an unknown planet. Solo managed a landing, and Rar and Organa Solo left the Millennium Falcon in full hazmat gear to drain out contaminated coolant into collection buckets. Jae Juun, the Sullustan who had been acting as the Solos' guide, brought out Rar's utility belt with her lightsaber attached; the Twi'lek and Organa Solo then set about draining the coolant from the freighter into the buckets.
Supported by Alema Rar, Plo schemed to turn the Galactic Alliance against the Killiks in the hope that Chief of State Omas would allow the Chiss free rein in dealing with the insectoids, leading to an uninterrupted war between the Chiss and the Killiks which Plo hoped to win. To further her chances of success, Plo manipulated Thul and the Killiks into building gigantic nest ships, so that the Killiks could leave the planets of the Woteba system, which possessed a troublesome ancient environmental defense system that prevented adequate colonization, and invade the Chiss Ascendancy. When, a year after the Dark Nest Crisis had concluded, the Skywalkers and Solos returned to Woteba to confer with Raynar Thul about the problems on the Woteba system's planets, Alema Rar was on hand to observe them. At the Saras hive on Woteba, where the Millennium Falcon was docked, Rar's foes prepared to leave following their discussion with Thul. Wary of possible Jedi interference, Plo and Rar had concocted a scheme to weaken the Jedi Order and planned to sow misinformation and doubt into the highest levels of its leadership.
When a band of Gorog insects and criminals who were smuggling reactor fuel for the nest ships was discovered on Woteba by Luke Skywalker and Han Solo, Alema Rar traveled to locate Raynar Thul in order to prevent the news from alerting the puppet Killik leader to the machinations of the Gorog. Although Skywalker and Solo, who arrived first, were initially successful in convincing Thul of the truth, Alema Rar telepathically persuaded Thul that the Jedi, not the Gorog hive, had brought the reactor fuel to Woteba, and that he was being deceived. Thul ordered his guards to converge on Solo and Skywalker, but the Jedi Master realized that Rar was present, and forced the Twi'lek to reveal herself. Grudgingly acknowledging Skywalker's abilities, the Twi'lek emerged and set about informing Thul and the Unu nest that the Jedi were sabotaging the Killiks and wanted the species eradicated. With the mental manipulation of the Gorog hive influencing him, Thul paid no attention to Skywalker's arguments to the contrary.
Rar then once again began to sow doubt in Skywalker's mind about his wife's loyalty, hinting that the former Emperor's Hand was concealing something important from the Jedi Master. She gave C-3PO, who was accompanying Skywalker, another code sequence, despite Solo's protestations, before implying that Mara Jade Skywalker could have been involved in the death of Padmé Amidala and subsequently leaving. Seconds after her departure, Gorog exerted its influence and wiped the memory of Rar's presence from the minds of Thul and the Killiks present. Skywalker and Solo were subsequently imprisoned. The code sequence Rar had given C-3PO was a holorecording from the Jedi Temple during Operation: Knightfall, when Anakin Skywalker, newly anointed as Darth Vader, had led the 501st Legion into the Jedi headquarters and massacred those Jedi present, including younglings.
Wounded and barely alive, Rar sought safety in a cave. With a fractured arm and six fractured ribs, as well as deep wounds in her abdomen and back, the Twi'lek was in a critical condition. To aid her in her recovery, she used the Force to summon Killiks to her which had survived the battle. A group of the insects arrived and cared for her over the course of the year. As each one completed their natural life spans and died, Rar recorded their deaths on a Twi'lek story-chain. By 37 ABY, the Twi'lek's injuries had healed. Although her body was lopsided and covered in thick scars, she was capable of walking. The healing of her injuries did not stop Rar from obsessing about those who had caused them. The Twi'lek descended into insanity, becoming fixated on avenging herself upon Luke Skywalker and Leia Organa Solo, and developed a unique philosophy known as the Balance. She came to believe that every action in the galaxy should have a counter-action; thus, she had to cause as much pain to Leia Organa Solo and her brother as they had to her. Rar did not believe that she was the agent or creator of the Balance, but that she could be guided by this intangible force in her actions. The Twi'lek came to the conclusion that she was still a Jedi, only now in service to the Balance.
Besides obsessing over how to gain revenge on her enemies, Rar also developed several other traits. She continued to refer to herself in the first person plural pronoun, which she believed honored the Gorog nest. As the last surviving member of the hive, the Twi'lek felt that referring to herself in the singular would prove that the nest was truly destroyed. She also began to talk aloud to herself. While on the planet, Rar constructed a blowgun and obtained from the wild Tenupian jungle some potent toxins, including a deadly poison and a flesh-eating bacteria. She cataloged the different substances she collected in vials, which she kept about her person. Near the end of her first year marooned in the Tenupian jungle, Rar caught a fever and entered a hallucinogenic state, dreaming that she was exploring the Massassi temples on Yavin 4 with her long dead sister, Numa. When the Twi'lek awoke, she was stranded high atop a mountain on the planet. 59ce067264