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The Second Jedi Civil War was an internal conflict within the New Jedi Order that quickly escalated into war on a Galactic scale.

The Jedi Exiles, tired of the Jedi Order's involvement in political masquerades, separated and moved to the abandoned Jedi Enclave on Dantooine. They delved into the teachings of Dark Jedi and Sith, however, and soon it became apparent to the New Jedi Order that the Jedi Exiles were a threat. When the New Jedi Order invaded Scovara on peacekeeping operations as a result of tension between the Scovara Combine and the Alliance, the Exiles gladly intervened, sparking the Second Jedi Civil War.

In 296 ABY, four hundred Jedi warships engaged the Jedi Exiles in a battle for control of the temple on the Force-planet Mortis deep in Wild Space.

The war ended with the betrayal of the Jedi by the Alliance, who saw them as a threat to galactic peace. The Senate decided that the Alliance had stayed out of the Jedi Order's internal struggles for too long, and vowed to put an end to it immediately. The Ranquell Peace Commission compiled a fleet of six thousand warships and set a course for Mortis to arrest the Jedi and bring a halt to the conflict. Their destruction of the sacred temple on Mortis was a mistake, however, that resulted in both the end of the war and the end of Galactic stability.