As a segment of the Second Galactic Civil War, the Second Battle of Fondor occurred in 41 ABY. Following Fondor's departure from the Galactic Alliance to join the Confederation, Jacen Solo, the Chief of State, resolved to reclaim the planet, along with its orbital shipyards, aiming to bolster his authority. This engagement marked the final time that Admiral Cha Niathal and Jacen Solo fought together as Joint Chiefs of State. The battle's outcome led to a schism within the Galactic Alliance, creating factions loyal to Darth Caedus and those backing Niathal. While the Imperial Remnant and a large portion of the Alliance fleet sided with Caedus, Niathal could only gather roughly a third of the remaining Alliance vessels to support her.
The battle concluded with the arrival of Admiral Natasi Daala and her Maw Irregular Fleet, who launched an assault on Caedus. Faced with being both outnumbered and outgunned, Caedus was forced to retreat. Subsequently, Niathal and Daala aligned themselves with the resistance against the Sith Lord.

Seeing an opportunity to depose Solo, Admiral Niathal secretly initiated communication with Grand Master Luke Skywalker concerning the Alliance's blockade around Fondor. This communication ultimately resulted in Luke Skywalker informing the Fondorians about the planned placement of space mines around their planet. The ships deploying the mines were subsequently destroyed, and Fondor prepared for an impending invasion. This significantly impacted the defense against the GA forces, as the mines could have swiftly eliminated numerous ships, thereby improving the planet's chances. Niathal later regretted her actions, which led to the deaths of one hundred soldiers due to her leaked information.
To ensure his victory, Caedus reached out to the Imperial Remnant, offering them Bilbringi and Borleias in exchange for their assistance in capturing Fondor. Grand Admiral Gilad Pellaeon promptly declined his offer. However, Caedus had anticipated this response and dispatched Tahiri Veila to sway him. Following a meeting with Veila, Pellaeon presented the proposal to the Moff Council. They sanctioned the aid to Solo, leading Pellaeon to accept the offer, which was met with approval from the Moffs. The Grand Admiral committed his forces to the battle. Still distrustful of Jacen Solo, he contacted Admiral Daala, requesting her personal fleet's support in case he needed protection from the Sith Lord or any other potential danger. Daala then contacted Boba Fett, asking him to bring his finest soldiers to assist her in the forthcoming battle.
As the GA's Fourth Fleet converged in the space near Fondor, Colonel Jacen Solo decided to reconnoiter the area in his StealthX. Niathal and her task force also arrived, but Solo suddenly detected a massive, unidentified fleet. It turned out to be an elaborate illusion crafted by Luke Skywalker using the Force. He alerted the crew of his ship, the Anakin Solo, as well as Niathal, about the supposed incoming fleet. Since Solo was the only one who could perceive the illusion, Niathal seized the opportunity to embarrass him in front of the commanding officers of his fleet. Luke Skywalker managed to severely damage Solo's StealthX by ramming it with his own starfighter before Solo could safely retreat into the Anakin Solo's hangar.

The battle commenced at midnight, with GA X-wings targeting the shipyards and patrolling frigates. Destroyers moved towards Fondor's north and south poles, while warships amassed in the orbital ring. Simultaneously, numerous Fondorian starfighter squadrons launched attacks from the planet's surface. Although the GA ships did not sustain significant casualties initially, Colonel Solo noticed numerous capital ships, likely deemed non-operational by the GA, beginning to mobilize. He realized that his task force was trapped between the orbital shipyards and the planet. The Fondorian fleet divided into two groups: one engaging the Fourth Fleet under Jacen Solo, and the other attacking the Third Fleet and the Imperial Remnant ships.
Niathal desired Solo to regroup beyond the shipyard ring, but he instead persisted in approaching the planet. Harnessing his full power, Solo employed the Force to mentally manipulate the Fondorians into deactivating the planetary shield located in Oridin City. This action significantly depleted his energy, leaving him exhausted.
After ensuring the shield could not be reactivated by ordering missile strikes, Solo instructed his ships to commence bombarding the city. The bombardment caused damage to six cities in the region and ignited massive firestorms. Niathal immediately contacted Fondorian President Shas Vadde, offering him the chance to surrender the planet. She promised that the GA would provide disaster relief for Oridin. Following a brief deliberation, Vadde surrendered, and both commanders ordered their forces to cease fire. Solo was informed of the surrender but refused to accept it, feeling that he had invested too much energy into bringing them to their knees, and continued his attack. Niathal, exercising her authority as Supreme Commander, relieved him of command for violating the laws of war and ordered the Alliance fleet to disobey him. However, two-thirds of the fleet remained loyal to Solo.

Concurrently, Pellaeon declined to continue attacking the surrendered planet and instead directed all Imperial Forces to obey the commands of Chief of State Admiral Niathal. Some of the Moffs aboard the Bloodfin with Pellaeon voiced their objections to these orders. Grand Admiral Pellaeon firmly stated that the Imperial forces would honor the Fondorian surrender. Tahiri Veila attempted to persuade him to aid Jacen, who was now outnumbered, but Pellaeon refused. Subsequently, Tahiri murdered him and was officially named Darth Caedus's Sith apprentice after she reported his death.
Following this, Grand Moff Quille, along with other Moffs, attempted to seize control of the Imperial Remnant warships and fight for Jacen Solo. However, the crew of the Bloodfin mutinied, and the Moffs loyal to Quille, along with Tahiri Veila, barricaded themselves in the central command sections of the ship.
After securing the loyalty of the Imperial Remnant and the majority of the GA fleet, Caedus launched an attack on Niathal. However, just as Caedus initiated the attack, Admiral Daala arrived, commanding the Maw Irregular Fleet that Pellaeon had prepared as personal backup. They supported forces loyal to Niathal in attacking Caedus's forces. Meanwhile, Pellaeon's new flagship, the Bloodfin, was successfully seized by Mandalorians led by Boba Fett. Quille and those officers loyal to him were killed in gunfights aboard. Tahiri Veila was successfully extracted by her new master and brought to safety as the Mandalorian commandos handed the Bloodfin over to Daala.
The remaining Imperial/Alliance forces loyal to Caedus were driven from the system and retreated to Coruscant after Darth Caedus realized they were outnumbered by thirty percent and many of Daala's ships were armed with powerful Metal-Crystal Phase Shifters and other unconventional weapons which they were not prepared to fight against. Luke Skywalker negotiated with the President of Fondor for Niathal to use Fondor as her base of operations for her faction of the Galactic Alliance, forming a united front against Caedus.
Following the battle, the Imperial Remnant demanded the return of Pellaeon's body, but Daala refused to comply and instead sent them the bodies of the Moffs, burying Pellaeon on his home planet of Corellia afterwards.
Four days after the battle, Darth Caedus controlled the Galactic Alliance from Coruscant. He now ruled alone, as he had always intended, and promptly began demonstrating his plans for the galactic government by abolishing laws that hindered him, such as the legal requirements for Security Council meetings.