The Second Galactic Civil War, alternatively known as the Corellia-GA war, Alliance-Confederation War, Confederation-Galactic Alliance War, Corellian-Galactic Alliance War, New Galactic Alliance War, New Galactic Civil War, the second Corellian Insurrection, or simply CivWar Two, lasting from 40 ABY to 41 ABY, was a conflict originally between the Five Worlds—which later grew to become an interstellar alliance known as the Confederation—and the Galactic Federation of Free Alliances. The conflict began when the Corellian system seceded from the Alliance over local defense limitations and increased taxes to pay for reconstruction in the aftermath of the Yuuzhan Vong War, and gained allies such as Bothawui, Bespin, and Fondor, forming the Confederation. As the conflict quickly escalated, the New Jedi Order battled the rebels alongside the Alliance. Many who had once been allies during the First Galactic Civil War and Yuuzhan Vong War found themselves on opposing sides during the conflict.
Eventually, many events in the war became uncontrollable, with a decisive fleet victory proving impossible. Amid months of desultory naval skirmishing, the Galactic Alliance Guard was formed in the name of state security, and under Jacen Solo's command committed acts such as the internment and assassination of dissidents that were increasingly viewed as dictatorial. In a coup, Admiral Cha Niathal and Colonel Jacen Solo ousted Chief of State Cal Omas and took his place on Coruscant. Corrupted by and apprenticed to the Sith Lady Lumiya, Jacen secretly became Darth Caedus, the new Dark Lord of the Sith after killing Mara Jade Skywalker. An attempt by the Confederation to push into the Core Worlds was halted at the Battles of Kuat and Balmorra, but the increasing authoritarianism of the GA's government led the New Jedi Order to withdraw from the Alliance, and in the aftermath of Caedus's actions at the Battle of Kashyyyk, they formed the Jedi Coalition. Following this battle, the war became a three-way conflict.
The war continued with the Galactic Alliance now facing two rebellious factions. The Jedi destroyed Centerpoint Station to prevent it from falling into Alliance hands but failed to capture Caedus. The latter allied himself with the Imperial Remnant, and a major battle occurred at Fondor, the Confederation's largest shipyard. During the Second Battle of Fondor, Grand Admiral Gilad Pellaeon was executed after refusing to obey Caedus's orders, and Niathal and her allies joined the Jedi Coalition as the Alliance-in-exile after refusing to bombard civilian population centers. Concurrently, Jedi Knight Jaina Solo trained under Boba Fett, leader of the Mandalorians, in order to take down her brother, who was by this time completely consumed by the dark side. As Caedus, Niathal, and the Confederation's forces continued to fight, Luke Skywalker planned to create a trap that would allow Jaina to kill her brother. In a climactic duel, Jaina defeated Darth Caedus as well as his New Sith Order. With Niathal's faction of the Galactic Alliance, the Jedi retook control of Coruscant and defeated Caedus' Alliance and Imperial faction, placing Jagged Fel as the leader of the Imperial Remnant. Tense relations between the Alliance and the Jedi resulting from the war continued in its aftermath, and the Confederation refused to formally rejoin the Galactic Alliance. To make things worse, Darth Caedus' actions had accidentally awoken Abeloth, the Mother of Chaos.
The Second Galactic Civil War was just the first of several galactic wars that disturbed the peace in the cosmos for a hundred years (40 ABY-140 ABY). The following wars were the Lost Tribe War, the galaxy's Second Cold War, Sith-Imperial War, Second Imperial Civil War and Darth Wredd's Insurgency.