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The exact cause of this war is unknown; halfway into it, most had forgotten what started it. During the war, alliances between the six species were constantly shifting, but in the end the Reptilians and Insectoids allied and planted explosives under Xindus's eight largest seismic fissures as a last, desperate act. This had the unintentional result of destroying Xindus due to its high geological instability. The Avians were unable to leave the planet and were wiped out. (ENT: "The Shipment")
The inter-species conflict resurfaced on February 12, 2154. The Reptilian Commander Dolim murdered the Primate Degra and stole the Xindi weapon. This second war ended two days later. Captain Jonathan Archer of the Earth starship Enterprise NX-01 destroyed the weapon before it could destroy Earth. The Primate, Arboreal, Aquatic, and Insectoid members of the Xindi Council agreed to reconvene after the incident, and expected that the Reptilians would eventually rejoin them as well. (ENT: "The Council", "Countdown", "Zero Hour")