- Juno Eclipse: "Blackout to Blackguard. Respond, please."
- Rahm Kota: "I don't have time to talk."
- Eclipse: "Bad luck. This is taking too long. You need to pull out."
- Kota: "Negative, Blackout. Leave if you want to. I'm staying to finish the job."
- ―Juno Eclipse and Rahm Kota, during a mission on Cato Neimoidia[src]
In 1 BBY, forces of the Alliance to Restore the Republic raided the planet Cato Neimoidia. Though composed of loyal members who were committed to the cause of restoring the former Galactic Republic, the fledgling Alliance was hardly considered as a threat against the well-organized and better-armed military forces of the Galactic Empire. As a result, the Alliance was forced to rely on guerrilla warfare—launching surprise attacks on unsuspecting Imperials and then retreating before enemy reinforcements could arrive.
Shortly after the Salvation was commissioned as the flagship of the Rebel fleet, former Imperial Captain Juno Eclipse was commissioned as its commanding officer. In order to test the battle readiness of the new starship and its crew, Captain Eclipse directed her vessel to Cato Neimoidia, a former Separatist world that became occupied by an Imperial garrison at the end of the Clone Wars. Unknown to all except Eclipse, Jedi General Rahm Kota and his squad secretly followed the flagship by utilizing the Rogue Shadow, Marek's old vessel that had been outfitted with a unique cloaking device for stealth purposes.
However, the raid not only failed to go as planned; it was a tactical disaster for the Rebellion. Alliance Intelligence severely underestimated the Imperial naval strength of Cato Neimoidia's garrison. Kota, unconcerned with the anomaly, proceeded to pilot the Rogue Shadow until he was planetside. Frustrated with the Alliance leadership's slow and overly cautious approach to war, Kota took it upon himself to assassinate Cato Neimoidia's oppressive governor, Baron Merillion Tarko, in order to undermine the Empire's reputation as an "invincible" state. After Kota bluntly ignored Eclipse's recommendation for a tactical withdrawal, a major explosion near Tarko-se caused the Rogue Shadow to disappear from the Salvation's sensors. Believing that Kota and his squad perished with Marek's starship, Eclipse ordered her ship to flee from the doomed fight via hyperspace and to rendezvous with the Rebel fleet near the Itani Nebula.
- "Soldiers of the Rebellion. Soldiers of The Salvation. This is the beginning. Remember this moment."
- ―Juno Eclipse, to the crew of The Salvation on the day of its inauguration
As the Galactic Civil War broke out with the formation of the Rebel Alliance, the Galactic Empire immediately sought to annihilate the latest threat to its primacy throughout the galaxy. In honor of the Alliance's founding father, the redeemed Sith assassin Galen Marek, Juno Eclipse committed herself to the overriding goal of the new organization—the restoration of democracy and the Old Republic. Formerly a captain and renowned pilot of the Imperial Navy, Eclipse was thrown into mourning after Marek's death, and thus she sought to ensure that his legacy would not die with him.
Due to her commitment to Marek's memory, Eclipse developed a sense of companionship with General Rahm Kota, Marek's unofficial Jedi mentor. Due to Kota's increasing disillusionment with the Alliance leadership's ineffective tactics, Eclipse allowed Kota to secretly accompany her on several assignments, thus allowing the Jedi to pursue unsanctioned missions. Despite the clear violation of protocol, Eclipse merely wished to ensure that Kota did not leave the Alliance out of frustration with its leaders.
After being commissioned as captain of the Rebel flagship, the Salvation, Juno Eclipse was commanded to initiate a test to oversee how well the new starship and its untried crew responded to the pressures of battle. However, she was also ordered to not allow any damage to come to the Salvation. Starships were incredibly hard to come by for the Alliance, thus making Eclipse's ship an invaluable asset to the struggling Rebel fleet. If the Imperial military presence on Cato Neimoidia posed a greater threat than anticipated, then Eclipse was obliged to withdraw from battle.
At the same, however, General Kota intended to take advantage of Eclipse's mission by undertaking one of his own—the assassination of Cato Neimoidia's corrupt governor, Baron Merillion Tarko. With a specially-trained squad as backup, Kota piloted the Rogue Shadow and stealthily accompanied Eclipse's ship. Due to the fact that Kota's objective was not authorized by the Alliance leaders, only Eclipse was aware of the Jedi's shadowy presence. She was even forced to deceive her first officer, Nitram, who had cleverly deduced that the Salvation was being followed by Kota in an unknown ship.
- "Sound the alert. I want twelve fighters strafing that city in the next five minutes Let's take the chance to strike while the Baron is busy."
- ―Juno Eclipse, issuing orders to the crew of the Salvation
Upon arriving at their intended destination, Captain Eclipse followed her instructions to the letter and immediately began testing Cato Neimoidia's defenses by dispatching a squadron of BTL Y-wing starfighters to engage a small group of Imperial TIE fighters. As General Kota executed his own objectives planetside, Eclipse covered up the Jedi's activities by dismissing them as a local insurrection to her crew, all of whom were oblivious to Kota's involvement in the raid.
However, it soon became apparent that Alliance Intelligence underestimated the planet's Imperial defenses as additional TIE fighters began to swarm the Rebel squadron. Outnumbered and caught by surprise due to misinformation on the Alliance's part, Eclipse was pressured into considering a hasty retreat from the fighting, especially to avoid risking the safety of her starship. But when she tried to warn Kota to retreat as well, the Jedi General dismissed her concerns about the Imperials' greater numbers and pressed his attack on Tarko-se.
Before she could attempt to persuade Kota into accepting a tactical withdrawal, an explosion near the city caused the Rogue Shadow to disappear from her ship's sensors. Eclipse instantly feared for the worst, and when Marek's old starship failed to appear once more on her radar, she assumed that it had most likely been destroyed—along with Rahm Kota and his men. After mournfully bidding the old Jedi farewell in the back of her mind, Eclipse ordered the bridge crew to take the Salvation into hyperspace, thus breaking off their attack and retreating to the Rebel fleet's secret location near the Itani Nebula.
- "We've got company. Two frigates, a cruiser, and—yes, a Star Destroyer, Imperial-class. Could be the Adjudicator. It's launching fighters. Captain?"
"Recall our pilots. Bring everyone aboard, then get us out of here, fast."
- ―Nitram and Juno Eclipse
As a result of the raid's failure and Rahm Kota's secret involvement with the mission, despite lacking authorization from the Alliance leaders, Captain Eclipse was temporarily relieved of her command. Though she contemplated thoughts of leaving the stagnant Alliance, which also caused her grief at the idea of turning her back on Galen Marek's legacy, Eclipse ultimately decided to serve the Rebellion in a fashion that was similar to Kota's approach—promote the Alliance's interest with or without the approval of its leaders.
Thus, she embarked on a mission with Bail Prestor Organa and his adopted daughter, Leia Organa to oppressed world of Dac. Since the Alliance was in desperate need of more manpower and superior ships, the three Rebels hoped to convince two of Dac's native races, the Mon Calamari and the Quarren. The mission not only succeeded in its objectives, but had also resulted in the recruitment of Admiral Ackbar into the Rebel fleet, as well as the Empire's own personal humiliation.
Contrary to Eclipse's belief, Rahm Kota and the Rogue Shadow survived the Imperial attack. However, with his squad dead and the Salavtion in retreat, Kota was unable to prevent his own capture. To amuse himself, Baron Tarko had the captive Jedi thrown into his city's arena. However, the Baron underestimated Kota's resolve and his command of the Force. Utilizing his skills with a lightsaber, the general fought wave after wave of gladiators and beasts. In spit of all his injuries and fatigued body, the aging Jedi continued to fight and triumph against all of his adversaries for several days straight, much to Tarko's frustration.
When Kota's capture on Cato Neimoidia reached the attention of the Sith Lord Darth Vader, he traveled to Kamino's Timira City Cloning Facility where, for the past six months, he unsuccessfully labored to create a more powerful and loyal version of his late apprentice, Galen Marek. After a series of failures and disappointments, Vader was in the process of training a highly stable clone of Galen Marek. The clone's development, however, was undermined by the imprinted memories and emotions that he inherited from his genetic donor—a side effect that drove all of the clones to develop identity crises, and ultimately utter madness.
Although Darth Vader originally intended to send the clone to Cato Neimoidia in order to kill General Kota, he was forced to deem him as yet another disappointing failure. Anticipating his creator's intention to liquidate him, the clone turned on Vader and ultimately escaped from Kamino. Having developed the same feelings for Juno Eclipse that Marek had prior to his death, the clone decided to rescue Kota from Cato Neimoidia, but only to discover where Eclipse was located.
- The Force Unleashed II novel (First appearance)
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