This alternative timeline is based on the premise that the Chosen One was in Arroyo when the Enclave capture team arrived and was either killed or captured; and that in the areas where the chosen has visited the "Most positive" outcome was in line to occur. Its also only the first part... Stay tuned for part 2 - Same Vault Place; same Vault Channel.
Edit: I realise there is a hole in the FEV timelime with regards to Canon. My bad.
Raspy Voice on. ---
Freed from the slaver Metzger; Vic returns to his old life of trading with tribals based out of his shop in Klamath. One of his journeys eventually takes him back to Arroyo where the spirit of Haunakin returns to his body to pass on one last message warning of the beginning of the end, this end coming from the west.
In his village, Sulik is trying to recruit a new team to assist in the search for his sister. When a hurried Vic arrives seeking help to interpret the shaman's last message, Sulik recognises severity of the message and agrees to again suspend the search for his sister for greater concerns.
The pair travel to Navarro; where Vic is able to put his old world technology knowledge to the good use and determines the Enclaves plan to release a virus into the atmosphere and locates the vaccine being used to inoculate the base staff. (As this occurs later than when the Chosen would have done in the core Fo2 timeline the plan is further down the track). Vic and Sulik take a sample of the vaccine and head for the only power they know may be able to do something about it - The NCR.
President Tandi calls an emergency council of all the NCR Govenors and military heads. The Republic's growing strain with the brotherhood is set aside and a representative is also invited into the meeting. A decision is made that whilst the Brotherhood and NCR will attempt to recreate the vaccine; the Vaults where possible will be prepared for immediate rehabitation.
Despite the NCR's attempt to keep this quiet, Westin leaks word to Vault City, who in turn abandon their city for the safety of the vault. The courtyard residents celebrate what they see as their liberation - rioting and looting is rife in the inner city until they realise that the Vault City citizens would not have left for the vault unless they believed the end of days were coming.
Although the former residents of the courtyard beg and plead to be admitted into the vault the actions of the days prior harden the citizens resolve not to admit the courtyarders. Remembering the stories of their grandfathers about nuclear fire liquidating whole cities, the courtyarders abandon Vault City and scatter in all directions and warn all they meet that the end of days is returning.
The NCR and Brotherhood send a joint team to Mariposa to obtain FEV samples. Recognising the severity of the threat the Brotherhood even permit some NCR researchers to use their prized powered armour for safety - what good is the codex if the end of days comes? The word is put out to all Western Brotherhood personnel not engaged in essential operations to return to Lost Hills, and any plans to send a team to DC are cancelled.
The Squat at V15 is evacuated at gunpoint to become the NCR's continuity of government centre. This coupled with the rumours from vault city begin to spread panic amongst the various towns. Those prone to believe in conspiracy tales begin to evacuate the cities, Mayor Ascortti starts selling homes in the Great Wannamango Mine. For their part, NCR officials deny any threat to the populace and invent stories to explain missing officials who have left for the Vault.
In Modoc after the stories of Vault Cities evacuation reach them before anyone else; the residents form a mob to demand access to the ghost farm's shelter. Eventually some sort of peace is brokered, but only after most on both sides have fallen. Similarly the residents of Klamath take to the caves under the mall.
In New Reno the Wrights evacuate to Sierra, but not unnoticed - they are followed by members of each of the families. In the 4 way battle that occurs the only true winners are the carrion eaters; those smart enough not to get shot form an uneasy truce and hunker down together. With no-one left to bring even a semblance of order, the town truly becomes a hell on earth.
Eventually the Curling strain of FEV is released. As the virus in this timeline has to disperse into the atmosphere, rather than a comparatively small oil rig the progress is slow. The Tanker Vagrants; Shi and Hubbologists are the first to die. The Brotherhood facility in San Francisco has been adapted to detect FEV the Brotherhood and their allies, signaling to the NCR that the seal on V15 should now be reestablished.
Those who sought shelter at the Ghost Farm; Klamath Mall, Redding mines or the Sierra Military Depot die. Whilst these might have provided decent shelter for a nuclear blast they have no protection against the FEV virus. The deaths spread eastward slowly across what was the continental US like as if a curtain is being pulled. Those who remained or reentered the vaults, or vault-like structures survive. Those who did not die.
In the Midwest the Brotherhood at Cheyene mountain detect the slowly increasing FEV count and take shelter in their bunkers. Where the bunkers offer full environmental protection they survive; but many are lost.
In our next exiting episode: The Enclave return to the CONUS.... Coming perhaps eventually, or perhaps only in a different timeline.