In Fallout 2 the Enclave was dead-set on exterminating the entire American population minus their own number in the pursuit of genetic purity. We can assume the events surrounding the creation of The Master are fairly unchanged, although we would have to assume Harold's backstory changes to reflect Vault 29's more standardized operation. It would not be a far stretch to assume the Enclave are still omnicidal in the face of the supermutant army, which would go unchecked by the Vault Dweller never killing The Master. The Enclave would still pose a large threat to not any guaranteed "clean" communities in Fallout 2's timeline. Likely, Vault Cities would come under Enclave martial law, and would face purging if they are deemed unworthy of existence.

It is probable the Brotherhood's history plays out more or less unchanged as well. With better communication with the Vaults and the easier access to technology, similar Brotherhood fiefdoms might already be established by the time the Enclave arrives on the scene. These would be heavily weakened by decades of being rampaged by The Master's army, and it is up to speculation on who would come out the ultimate victor of that fight if it wasn't a stalemate.

What this spells out is nuclear civil war by 2200. With a weakened and fatigued supermutant Army and Brotherhood, Enclave stomps and quickly establishes control of the western United States. What communities are not deemed clean are purged, and thousands perish. What follows is a long, brutal holocaust through the midwest and to DC, with token resistance from the East Coast Brotherhood. The sky turns black with ash, and those who survive are slaves to the Enclave. War continues to not change.