NCR flag (left) and Enclave symbol (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 began when an unknown amount of time had passed after the canonized events of Fallout 2, and ended sometime after with the decisive sacking of Navarro. Details and specifics on when and how this conflict occurred and/or played out remains a mystery.
Several years after the Chosen One destroyed the Control Station ENCLAVE Oil Rig, the NCR ultimately decided that Navarro along with the rest of the local Enclave personnel would constitute a threat to the security of the region despite being cut off from their leadership, proceeding ahead with a widespread offensive.
The NCR would sack the previously heavily defended Navarro outpost, inflicting a decisive blow to the remaining Enclave presence in California, despite suffering horrendous casualties. From there on, the NCR, while bilateral relations with the Brotherhood remained agreeable, continue with hunting down the surviving Enclave forces within the known territory.
While the majority of the Enclave would relocate to a lot of different places according to Arcade Gannon, most noteworthy being the Capital Wasteland, some would go into hiding while the remaining few who were not exposed, arrested or killed in battle or otherwise, successfully integrate into the NCR.
The Brotherhood would assist the NCR in arresting those that were caught for war crimes and as a result, relatively few managed to live in NCR territory by hiding.
Remnant Enclave personnel lingering in California that did not relocate with the rest of the Enclave, successfully disappear, or integrate into the NCR, were ultimately arrested and tried as war criminals. Some would even be 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 knowledge of the area.
Due to the NCR's use of Enclave equipment taken from Navarro they could not understand, they would eventually, via the Courier, bring about the destruction of the Divide, killing an unknown amount of people in the area.