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NCR flag (left) and Enclave emblem (right)
Though they were a powerful force in the west decades ago, the Enclave has not been seen or heard from in the Mojave Wasteland for years. Members who were not hunted down are believed to have traveled east - or successfully integrated into the NCR.”— Loading screen
The NCR-Enclave War was a military conflict between the temporarily aligned forces of the New California Republic and the Brotherhood of Steel against the remaining Enclave personnel on the West Coast. 
The war ended sometime after with the decisive sacking of Navarro.  Details and specifics on when and how this conflict occurred and/or played out remain a mystery.
Sometime after the Chosen One destroyed Control Station ENCLAVE, the NCR ultimately decided that Navarro, along with the rest of the local Enclave personnel, would constitute a threat to the security of their region, despite being cut off entirely from their leadership, proceeding with a widespread offensive.
The NCR sacked the previously heavily defended and fortified Navarro outpost, inflicting a decisive blow to the remaining Enclave presence in California, despite suffering serious casualties. 
The majority of the Enclave, according to Arcade Gannon, was able to relocate to a wide array of different locations. The most noteworthy examples would be in the Capital Wasteland and according to ED-E, Chicago. Some went rogue, and/or into hiding. The remaining few who were not exposed, arrested/executed, or killed in combat or otherwise, successfully integrated into the NCR.
Remnant Enclave personnel lingering in California that did not relocate with the rest of the Enclave, successfully disappeared, or integrated into the NCR, would ultimately be arrested and tried as war criminals by the NCR, and eventually imprisoned indefinitely, or even executed. Some were able to slip through NCR territory into Nevada.
At least one sizable bunker is known to remain in operating condition in the Mojave Wasteland, serving as a small base and refueling station for Vertibirds, with not only the NCR but the Mojave Chapter of the Brotherhood evidently failing to find or gain any sort of knowledge of the area despite controlling areas extremely close to its location.
Ultimately, the combined successes of the NCR-Brotherhood alliance in their mutual efforts against what remains of western Enclave activity would not last, as not long after, the NCR-Brotherhood War would be declared. Due to the NCR's taking of and usage of Enclave technology from camp Navarro that they could not understand, they would ultimately, via their unaware employee, bring about the destruction of the Divide, killing an unknown amount of people within or near the area of proximity.