Unity crisis

The Unity crisis was the rise of the Master and his army, with an ultimate goal of converting all of humanity into Super Mutants.

Origins of the Unity
Richard Moreau was a resident of Vault 8, later known as Vault City, where he worked as a doctor. In 2092, he was exiled from the city. He changed his name to Richard Grey and headed south, eventually settling in the Hub, where he met Harold, a prominent trader. Following ever increasing attacks on Harold's caravans by mutated creatures, the pair teamed up on May 22, 2102, and led a team of scientists who mounted an expedition to the northwest to investigate the source of the mutated animals, which were attacking the survivors of the war. On June 23, 2102, Grey and his party stumbled upon the Mariposa Military Base, in which the U.S. government had been mass producing and experimenting with the Forced Evolutionary Virus (F.E.V.).

With the exception of Grey and Harold, the party was cut down by the mutated creatures and the base's internal defense systems. Harold barely escaped, but Grey was plunged into a vat of F.E.V. by a robotic arm. Floating in the vats for almost a month, the F.E.V. transformed Grey into the amorphous, blob-like being that would eventually become known as the Master. This entity expanded its biological mass by absorbing other creatures and people that came near the base, and bionically merging itself with computer equipment from the base. The ones he consumed also became part of his multiple personalities. It also began capturing humans that stumbled upon its lair, and intentionally exposing them to the F.E.V. These initial mutated humans were incredibly flawed, and the newly named Master consumed them rather than letting them live.

As he began to feel stronger and more capable than ever before, he came up with the idea to 'unify' the wasteland, to make it as perfect as he believed himself to be. In January of 2103, the Master perfected his method of infecting, or 'dipping', humans, and began creating the super mutants, who followed the Master's every command. Unfortunately for him, as he began to dip others in the vats he found the resulting creatures were not like himself: most often, they mutated into brutish soldiers, losing much of their brain function. It became apparent that only those with low total radiation count would not suffer this fate.

Crisis
In 2130, the Great Winter occurred, causing a scarcity of human subjects for dipping; therefore making it difficult for the Master to expand his army further. From 2131 to 2135, the Master started to abduct caravans for human subjects. Most of the caravan disappearances were blamed on desert monsters, steering away suspicion. Starting in 2137, the Master began to mass produce super mutants with 1 in 6 being successful super mutants, and only this sixth making it into the Unity.

Around 2151, the mutants destroyed the Union of Atomic Workers. From there, the Master's Army mobilized and slowly began a conquest of the Core Region.

In 2152, as the influence of the Master's army began to spread throughout the wastes, the Master came into contact with a group of human Doomsday cultists, led by a man named Morpheus. Realizing the benefits of retaining unaltered humans in his service to act as spies throughout the region, the Master recruited Morpheus's cult into his service, thereby expanding his power.

Vault Invasions and the Rise of the Cathedral
The Master, having discovered that pure strain humans had better chances of retaining their intelligence and strength upon being mutated by the FEV virus, began a conquest for humans without radiation exposure. He quickly determined the best source of pure human stock: the vaults.

Vault 17 was raided in 2154 by the Master's Army, and its inhabitants were taken prisoner and subsequently turned into super mutants.

In 2155, the Master discovered the location of an unnumbered experimental Vault-Tec vault prototype, located just south of the center of the ruins of Los Angeles, California, now called the Boneyard. Seeing great opportunity there, the Master relocated to the vault with his human cult followers and a portion of his ever-growing super mutant army, and oversaw the building of a large cathedral on the surface above the vault the following year. The cult became known as the Children of the Cathedral, and continued to be led by Morpheus, who reported directly to the Master. The Cathedral was guarded by the nightkin, which were super mutant elite troops equipped with Stealth Boy technology.

In 2157, the Master learned the location of Bakersfield's Vault 12, and in order to further his plans, he sent a detachment of super mutants there to seize the Vault. Many ghouls were snapped like twigs in the attack, until Set, leader of Necropolis, finally parleyed with the super mutants, telling them that the ghouls were the vault dwellers the super mutants were looking for. The super mutants, angered at failing to find an intact Vault, set up a small garrison at the watershed to watch the inhabitants and ensure Set's cooperation in the further advancement of the Master's dream.

Growing Opposition
Few stood up to the Unity, because the existing factions in the wasteland at the time didn't possess the power, knowledge or resources to fight off the threat to humanity. Many weren't even aware that the mutants existed.

Around 2161, the Followers of the Apocalypse were one of the few groups to suspect that the Children of the Cathedral had ulterior motives. Despite their claims of having peaceful intentions, the emergence of the Children coincided with a sudden surge of unexplained disappearances, especially of those who objected to their cause. Talius, a ghoul-like mutant partially exposed to FEV by the Master's forces, found refuge among the Followers, and helped them understand the true nature of the Children and the "Dark God" they served. Although pacifists by nature, the Followers were determined to stop the Master's plans by any means necessary, even if it meant resorting to armed conflict. They began secretly gathering intelligence on the organization that could prove useful in the upcoming showdown, using one of their members to infiltrate the organization and spy on them. They also provided informational and material support to those who sought the destruction of the Master and the Cathedral.

The Brotherhood of Steel only learned of the Super Mutant threat until fairly late into the Unity's conquest of the Core Region, and even then did not openly engage the Master's Army. Brotherhood patrols sent south towards the Boneyard never returned. High Elder John Maxson expressed a desire to fight the mutant armies, but he and the other four elders couldn't come to a consensus. In October of 2161, a Brotherhood patrol stumbled upon the corpse of a Super Mutant. The remains were transported back to Lost Hills for study by Head Scribe Vree. Because of their knowledge that the mutants wouldn't be able to reproduce, Vree recommended to simply let them die off. The Brotherhood didn't engage the Master's army until the arrival of the Vault Dweller.

Entrance of the Vault Dweller
Vault 13's overseer, Jacoren, sent the Vault Dweller out on a mission to find a replacement for the vault's broken water chip on December 5, 2161.

On February 13, 2162, the Vault Dweller found the water chip in Vault 12. When in Necropolis, he engaged the Super Mutant garrison that was set up there. One mutant with a flamethrower killed his companion, Ian.

Upon returning to Vault 13, the Overseer told him that the amount of super mutants located in the area did not match up with natural rates of mutation. Believing that someone must be artificially creating the super mutants and fearing for the safety of the vault, he ordered the Vault Dweller to find and destroy the source of the mutants.

Death of the Master
The Master's Army attacked Necropolis and killed the majority of its inhabitants shortly after the Vault Dweller's departure from the city. He was told that the Master's Army was looking for him, and that he had become known as an enemy of the Unity.

On March 3, the Vault Dweller successfully infiltrated the Cathedral. The Cathedral was destroyed in an atomic explosion which could have been caused by the Vault Dweller sneakily detonating the nuclear weapon within the demonstration vault, or by the Master himself after being convinced that his plan would fail. The Master also could have been simply killed in combat, with the bomb being detonated as a part of a self destruct sequence.

Destruction of Mariposa Military Base
The Vault Dweller soon found Mariposa Military Base. Causing an explosion in the F.E.V. vats on March 24, he single-handedly destroyed the Lieutenant of the Master's army as well as the Unity's ability to produce more mutants. Dogmeat was killed during the infiltration of the base, running into a force field and being electrocuted to death.

The mutant threat had been abolished. The Unity Crisis was over, but its effects would change and shape the wasteland for years to come.

Aftermath
Shortly after the destruction of Mariposa Military Base, most of the survivors of the mutant army fled to the east. Several mutants led their own armies after the fall of the Master. Remnants of the Master's army, such as those led by Tabitha, were found to relocate to inhospitable regions such as Black Mountain. However, despite their lacking numbers and remote locale, they were still found to pose a threat to the populace of the Mojave Wasteland due to frequent and brutal attacks carried out against travelers.

Gammorin led many mutants into the midwest, where they were pursued by the Brotherhood. This led to the creation of a splinter faction of the Brotherhood and a long, drawn out war between Gammorin's Army and the new Midwestern Brotherhod of Steel.

Attis led another group down to Texas, seeking to revive the Master's dream.

In 2236, Enclave troops stumbled across the old abandoned Mariposa Military Base. The Enclave excavated the military base, largely using a workforce of miners gathered from surrounding locales that eventually found the vats deep inside the lower levels of the base. Though they had been buried in rock and forgotten for decades, the vats still contained the Forced Evolutionary Virus. The Enclave gathered samples to be sent back to their oil rig for further analysis and study. They found that it would be possible to make from FEV an incredibly potent and lethal toxin that only affected humans with even slight radiation exposure. Thus, they generated a plan to launch the poison into the jet stream of their base to kill off the entire known population of the mainland.

Interestingly, despite the Vault Dweller playing the largest part in the defeat of the Unity, the New California Republic disregards his canonicity.