The Swarm War, a relatively short, yet incredibly destructive conflict, transpired in the uncharted territories of the Unknown Regions and the untamed expanses of Wild Space during the year 36 ABY. The combatants were the Chiss Ascendancy, backed by the Galactic Federation of Free Alliances and the New Jedi Order, against the Colony, a collective force comprised of the insectoid Killiks and their Joiner collaborators. This war was essentially a continuation of the events that unfolded during the Dark Nest Crisis in 35 ABY. Despite the Galactic Alliance's attempts to forge an alliance with the Chiss, some Jedi factions sided with the Killiks; consequently, the Chiss suspected the Alliance of aiding the Colony, although they largely accepted the Alliance's assistance.
Efforts aimed at averting the outbreak of war were thwarted when Jedi Knight Jacen Solo launched an assault on a military supply base belonging to the Chiss Expansionary Defense Force. His intention was to provoke them into launching a preemptive strike against the Killiks. The Killiks retaliated by attacking Galactic Alliance forces that were blockading the Utegetu Nebula. Following the defeat of the Killik forces in that sector, the Galactic Alliance formally declared war on the Killik colonies.
The Killiks rapidly amassed allies to bolster their forces for the impending war. In addition to the numerous Joiners who had succumbed to their influence during the Yuuzhan Vong invasion, many members of various insectoid species throughout the galaxy's populations (including the Fefze, the Vratix, the Yam'rii, the Verpine, and the Geonosians) fell under their sway and became addicted to the Dark Nest's black membrosia. Many of these individuals also became Joiners, often at a much faster rate than their humanoid counterparts.
During the conflict, the Galactic Alliance forces were under the command of Supreme Commander Gilad Pellaeon (who had succeeded Sullustan Sien Sovv, who tragically died in an accident involving the Killiks a few weeks before). The New Jedi Order was led by Grand Master Luke Skywalker.
One of the key battles during this period was the conflict on Thyferra, where a coup led by tarhead Vratix, who were controlled by the Killiks, resulted in a complete shutdown of the production of the vital healing substance known as bacta. Despite this setback, the Alliance eventually regrouped and emerged victorious.
However, the war led Luke Skywalker to the realization that the New Jedi Order had become excessively entangled with the political affairs of the Galactic Alliance, compromising its core mission to uphold truth and justice, similar to how the Old Jedi Order had become overly involved with the politics of the Galactic Republic. As a result, he proclaimed himself Grand Master of the Jedi Order and established a new Jedi Council to provide guidance to the Galactic Alliance government. Furthermore, he withdrew the Jedi from Cal Omas's Advisory council, asserting that the Jedi's role should be to serve, not to govern.