History of the Brotherhood of Steel

The Brotherhood of Steel are a techno-religious faction in North America, whose main mission is to recover pre-war technology. They have a long history with roots stemming from the United States Armed Forces.

History
The founder of the Brotherhood of Steel was Captain Roger Maxson of the United States Army. He was a member of a military team commanded by Colonel Robert Spindel, originally sent to the West-Tek research facility on January 3, 2076 by the U.S. Army to monitor the experiments being conducted there by West-Tek on behalf of the American government in the interest of national security. On January 7, 2077, all West-Tek military research was moved to the newly-constructed Mariposa Military Base, along with Spindel's team, to enhance the research's security.

On October 10, 2077 Captain Maxson and his men discovered, to their horror, that the West-Tek scientists at Mariposa were using military prisoners as involuntary test subjects in their experiments with the genetically-engineered Forced Evolutionary Virus. Morale in the base broke down, and Colonel Spindel suffered a mental breakdown, eventually committing suicide five days later. Captain Maxson's men turned to him for leadership in the midst of the crisis.

After interrogating Robert Anderson, the chief scientist on the West-Tek research team, and learning about the extent of their scientific experiments on military prisoners, Maxson executed Anderson in disgust, and the other scientists soon followed their leader to the firing squad. Maxson, now in control of the entire Mariposa base, declared himself to be in full desertion from the U.S Army via radio on October 20, 2077. Strangely, he got no response from the Army chain-of-command, as the rest of the Army was too busy fighting the Chinese threat. Three days later, on October 23, 2077, the nuclear arsenals of both sides were launched, and the Great War ended two hours after it started, with most of the Earth reduced to a radioactive wasteland.

The Mariposa Military Base survived the nuclear exchange that devastated the United States, the soldiers within protected from the radiation and FEV flooding into the newly created Wasteland by the base's highly-effective nuclear, biological and chemical weapons protection protocols. Two days later at Mariposa, on October 25, 2077, an Army scout in Power Armor (Platner) was sent out to get specific readings on the atmosphere. He reported no significant amounts of radiation in the area surrounding the facility. After burying the bodies of the executed scientists in the wastes outside of Mariposa the soldiers sealed the military base, then headed out into the desert, taking supplies and weapon schematics from the base with them. Captain Maxson led his men and their families to the government fallout bunker at Lost Hills in California (this event was later called the Exodus). In November 2077, after a few weeks in the Wasteland, the soldiers and their families arrived at the Lost Hills bunker, suffering many casualties along the way from the terrible conditions of the Wasteland, including Maxson's wife (but not his teenage son). The Lost Hills bunker became the headquarters of the newly formed paramilitary organization that Maxson created and named the Brotherhood of Steel, intending to use its resources to eventually rebuild human civilization—no matter the cost.

Early Years
Little is known about the early years of the Brotherhood of Steel. In 2134, a faction led by Sergeant Dennis Allen gained strength in the organization, and urged the Brotherhood's Elders to let them explore the southeast ruins of the primary West Tek Research Facility, now called the Glow after it was directly hit by a Chinese nuclear bomb, for technological artifacts. The Elders refused, so Sergeant Allen and his separatist faction split away from the Brotherhood of Steel, taking some advanced technology and weapons with them. Despite that, under the leadership of Roger Maxson, the Brotherhood grew in strength, further developing their technology, and the orders of Knights, Scribes, and Paladins were formed. In 2135, Roger Maxson died of cancer, and his son took over as the new High Elder of the Brotherhood.

In the 2150's, the Brotherhood established its control over the areas surrounding the Lost Hills bunker, becoming one of the major powers in the Core Region of the West Coast. Some time in the early 2150s a raider group known as the Vipers began to establish a power base in the badlands to the south of the Lost Hills Bunker. Driven by a religious frenzy (and the need to provide for their much larger numbers of soldiers and disciples), they began raiding more frequently than before, eventually attracting the attention of the Brotherhood of Steel.



In 2155, the Brotherhood sent out a few squads of scouts to track the Vipers down. This was more of a training exercise conducted by the High Elder than anything else, as the Brotherhood was convinced that a small detachment of troops in Power Armor would be sufficient to deal with a group of raiders, no matter how large. One Brotherhood squad, led by High Elder Maxson, found the Vipers. Expecting the raiders to break and run at the sight of soldiers in Power Armor, Maxson did not take into account the religious zeal and ferocity of the Vipers...or their poisoned weapons. A single arrow nicked him while his helmet was off, causing him to die a few short hours later. John Maxson, the grandson of Roger, took up the role of High Elder, and Rhombus became the new head of the Paladins and the order of Knights.

The Paladins, now led by Rhombus, began a full scale campaign against the Vipers, tracking them down and wiping out almost all of their members within the span of a month. Some of the Vipers were able to flee north and east into the Sierra Nevada mountain range.

During the campaign, the Brotherhood sent a few scouts and emissaries to the Hub to track down the Vipers' members, and from these beginnings, the Hub and the Brotherhood opened full trade relations (caravans had delivered to the Brotherhood before, but not long after the destruction of the Vipers, caravan trains ran directly from the Hub to the Brotherhood's headquarters at Lost Hills on a regular basis).

The Super Mutants


Several years later, the Brotherhood faced an enemy far greater than any band of raiders. In October of 2161, a Brotherhood of Steel patrol came across a dead super mutant in the badlands. They took the corpse back to the Scribes, and Head Scribe Vree began to study it. After several long examinations, it was shown to be completely sterile.

In 2162, the Vault Dweller arrived at the Brotherhood's base at Lost Hills, wanting to join them. He was not taken seriously and sent on the usual fool's errand to the ruins of the West Tek Research Facility, renamed "The Glow" after a Chinese nuclear attack during the Great War made the facility a radioactive death trap. He surprised everyone by not only returning alive, but also succeeding in his mission (he was tasked with finding a holodisk with the record of an expedition of several Brotherhood Paladins to the Glow). As a result, he was the first outsider in a very long time to be accepted as a member of the Brotherhood of Steel, even though some prominent members of the Brotherhood resisted his joining the organization.

It was from the Vault Dweller that the Brotherhood learned about the Master's mutant army and his plans to turn all human survivors into super mutants. With the support of High Elder John Maxson, the Vault Dweller managed to convince the Council of Elders to send a squad of Paladins to the Mariposa Base (which had been, ironically, where the Brotherhood originated, although not even Maxson was aware of that), where the Master's FEV vats were located. With the help of the Brotherhood, the Vault Dweller eventually managed to defeat the Master, and was never seen again in the Lost Hills bunker. The Brotherhood at this time appeared to be the most technologically advanced faction encountered in the Core Region of the West Coast. Although the super mutant army and the Gun Runners had access to more advanced weaponry, the Brotherhood had a monopoly on Power Armor, certain medical technologies like cybernetics, and advanced supercomputers.

Aftermath
Following the defeat of the Master, the members of the Brotherhood began disputing amongst themselves over the need for new recruits versus their secrecy as an organization. The Elders finally ruled against the sharing of technology with outsiders, believing that they would continue to survive on their traditional principles. The minority that was opposed to this was sent eastward to track down the remnants of the Master's army via airships. When these airships crashed near Chicago, this group founded a new contingent of the Brotherhood of Steel. The Brotherhood would later establish small outposts throughout the California area, as well as carry out expeditions to Washington D.C. in 2254 and the Mojave later on.

Also following the defeat of the Master, the New California Republic was founded and began expanding. Eventually, the NCR founded the state of Maxson in the surrounding area of the Lost Hills Bunker. While the bunker remained under Brotherhood control, the state was under the jurisdiction of the NCR. Relations between the two factions weren't without tensions, but the two remained at peace for the time being.

The Enclave
By 2242, the Brotherhood was no longer the power that they once were. And with the reemergence of the Enclave, they were no longer the most advanced organization in the wasteland, knowing this, the Brotherhood was intimidated. Without the proper resources to deal with the Enclave, the best the Brotherhood could do was keep an eye on them; to this end, several bunkers near areas of Enclave activity were reactivated.

Eventually, the Brotherhood learned of the Enclave's vertibird technology. Without similar technology of their own, the Brotherhood would be unable to counter a possible Enclave invasion. At the request of his superiors, Matt of the San Francisco bunker enlisted the help of the Chosen One in retrieving the vertibird plans from Navarro.(Chosen One can refuse this, or just not complete the task outright. It doesn't conflict what was Chosen One's choice in Fallout canon.) If The Chosen One completed his mission successfully, but it is unknown whether or not these plans ever reached the High Council, as Matt was killed by Frank Horrigan a short time later. However, with the destruction of the Oil Rig and the NCR hunting down the surviving members, the Enclave ceased to be a threat (at least on the West Coast).

War with the NCR
By 2231, Jeremy Maxson had assumed the position of Brotherhood High Elder. In addition to wanting to expand Brotherhood operations eastward, he was much more aggressive in his "hoarding" of pre-war technology. He wanted to restore the power of the Brotherhood by wresting all advanced tech from the hands of "lesser people" by any means necessary. Naturally, this led to disputes with the NCR, which had always been in favor of using advanced technology for the benefit of society (at least according to Thomas Moore, an NCR citizen, which is what he saw as the NCR's justification for trying to annex Vault City). Shortly after the destruction of the Enclave, a war broke out between the Brotherhood and the NCR.

With their superior technology, the Brotherhood managed to hold out against the NCR, even coming close to total victory. Yet, the Brotherhood's technological advantage was eventually outdone by the sheer size of the NCR's army; no matter how many troops the NCR lost, they always seemed to have more. The Brotherhood, on the other hand, was still a selective group, and thus, was short on numbers. With this discrepancy in troop numbers, the Brotherhood's defeat was imminent.

The Mojave chapter of the Brotherhood of Steel would still be fighting the NCR as late as 2274. After establishing a base at Helios One, the Mojave Brotherhood soon found themselves at odds with the NCR and its growing power in the region. Eventually, the NCR sought to control Helios One, and the Brotherhood, under the orders of their Elder, Elijah, refused to leave. This led to a confrontation between the two, and in the typical chain of events, the Brotherhood's superior technology was no match for the NCR's superior numbers. Defeated in one of the bloodiest battles in the Brotherhood's history, in which over half of the chapter was killed, the Brotherhood retreated to the Hidden Valley bunker, where Nolan McNamara (in light of Elijah's disappearance following the battle) took the role of Elder upon himself, and placed the bunker under lock-down. Since then, the Brotherhood's presence in the Mojave Wasteland has been confined to only a few scouting missions.

Elijah set up a plan and fortress in the Sierra Madre resort. His goal was to break into the casino vault by capturing anyone foolish enough to set foot into his traps, collar them, and force them to do objectives to help break inside. His objective was to use the casino to send The Cloud soaring over Nevada and California, suffocating everybody, so that soon the Brotherhood could truly occupy the areas when The Cloud cleared and everybody had died. However, his plans were vanquished by The Courier.

The Expedition
In the year 2254, some time after the destruction of the "west coast Enclave", the Brotherhood's ruling council, based in the Lost Hills bunker in Southern California, decided to send a contingent of soldiers all the way to the East Coast, with three important objectives. First, to scour the ruins of Washington D.C., once the nation’s capital, to recover any and all advanced technology. Second, to investigate the reports of super mutant activity in the area, and third, to re-establish contact with the Midwestern Brotherhood of Steel and return them under Lost Hills command.

And so a small but hardened contingent of Brotherhood of Steel soldiers, led by an idealistic Paladin named Owyn Lyons (and accompanied by his friend and technological adviser Reginald Rothchild, as well as his three-year old daughter Sarah) set out from the Lost Hills Bunker in California, and began the long trek east to what was once Washington D.C.

Scourging the Pitt
Contact with the "rogue" Midwestern Brotherhood in Chicago turned out to be unsuccessful. On their way to the Capital Wasteland, the Brotherhood's East Coast expeditionary force came across the post-Great War slaver settlement known as The Pitt located in the ruins of what had been Pittsburgh, Pennsylvania. As the next morning dawned, the Brotherhood came over Mount Wash and razed the city to the ground. The Brotherhood were out-manned and out-gunned but they managed to fight their way through anything that put up a fight with barely a scratch.

Along the way they gathered up every non-mutated human child they found. In all, there were only twenty of them. Most were recruited into the Brotherhood. One, Greg Bear, is stationed with Lyons' Pride and is the only one of the children rescued from the Pitt left in the Capital Wasteland. This hints that the Brotherhood may have spread out more after the Pitt.

One member from Lyons' squad, Ishmael Ashur, was knocked unconscious during the battle against the slavers and buried in the rubble of the Pitt. The rest of the squad continued onward, leaving him for dead. Later, a group of raiders poked around the battle site as Ashur arose from the rubble. The raiders saw him as a godlike being, coming out from the rubble unharmed. Ashur then managed to take control of the Pitt after the Scourge had taken out the worst of the worst. Ashur managed to reactivate the old steel mills, and used the new industry to buy slaves from all over to continue the manufacturing work.

There are five holotapes in the locked safe in Ashur's room in Haven that contain a pre-recorded message from Ashur to his daughter, Marie. In these tapes, Ashur explains that he was pulled out of the rubble by a scavenger trying to take his power armor. The scavenger and their family often made raids deep into the ruined city for supplies. Ashur - looked upon by the scavengers as a god because of his power armor and Brotherhood of Steel technological know-how - took advantage of this and began to build a new city. As the city grew, raiders often attacked, and Ashur would kill the leader then recruit the others to serve as his guards.

Arrival
When the group finally arrived in the Capital Wasteland, it did not take long before they made some remarkable discoveries.

The Pentagon, as they had feared, was largely destroyed. But its sub-levels remained intact and contained enough pre-Great War technology and weaponry to keep Lyons’ forces going indefinitely (once the defense robots were destroyed). But there was something else, as well: Liberty Prime, a technological marvel that, if restored, could help the Brotherhood of Steel rebuild a strength and reputation that had been declining steadily for years.

The discovery was significant enough to earn Paladin Lyons a battlefield promotion to Elder, and a new directive from his superiors in Southern California – to establish a new, permanent Brotherhood base in the Capital Wasteland, and continue the search for any other advanced technology hidden in the former capital city’s ruins.

Lyons accepted his new post gladly, and founded the Citadel, built into and beneath the ruins of the Pentagon. It was a fortress the Brotherhood of Steel desperately needed, and one they rushed to fortify, thanks to their other great discovery in the Capital Wasteland. Super mutants also existed on the East Coast.

The Super Mutant Threat
It did not take long for Elder Lyons and the Brotherhood of Steel to find the super mutants, mostly because they didn’t have to look: the Super mutants found them. In the Capital Wasteland, particularly in the urban ruins of downtown D.C., the super mutants were simply too numerous to be avoided.

That is why, for the people of the Capital Wasteland, the arrival of the Brotherhood of Steel became the answer to their prayers. Scattered, hungry, and largely disorganized, they had lived with the constant threat of death or capture by the super mutants for as long as they could remember. Elder Lyons and his brave Knights and Paladins changed all that. For the first time, the super mutant tide was stemmed and forced back into the ruins of Washington. The D.C. ruins remained Super Mutant-controlled and uninhabitable, that was true, but the number of incursions against the outlying wastelander settlements dropped significantly. Life was still harsh and unfair, but at least now the people of the Capital Wasteland had a fighting chance, and they had Elder Lyons and the Brotherhood to thank for that.

New Objectives
Fighting the super mutants, or simply keeping them at bay, may have been enough for the region’s innocent wastelanders, but for the Brotherhood, too many questions remained: how had these local super mutants been created? Were they related to the super mutants of the Core Region in the west? Why were they capturing the people of the Capital Wasteland? Where were they taking them? Finding these answers would ultimately, become Owyn Lyons' obsession.

The years passed, but not in a way anyone had foreseen. Indeed, the Brotherhood of Steel’s importance to the people of the Capital Wasteland was not something that Lyons had ever expected. Nor was it something his Brotherhood superiors back in California cared at all about. Their newest Elder had a clearly defined mission – to acquire advanced technologies in and around the ruins of Washington D.C. Finding the source of the super mutant threat and destroying it was important too, of course. But it was assumed that the Brotherhood could easily eliminate the super mutants and their source fairly quickly. For the Brotherhood leadership, Elder Lyons’ prime objective was, first and foremost, the acquisition and preservation of pre-Great War technology. The super mutants were his second priority. This was the subject of every communication from the Brotherhood of Steel leadership in California.

But Elder Owyn Lyons had another priority, one he considered more important than his original directive or any orders received since – the protection of the innocent people of the Capital Wasteland. And so, Lyons sent word to his superiors that he would continue his search for technology when he was damned good and ready, and would not sacrifice the people who had come to rely on the bravery and strength of the Brotherhood of Steel.

The Californian corridors of the Brotherhood's Lost Hills headquarters erupted in rumor and speculation. Had Owyn Lyons “gone native,” putting the needs of the people of D.C. above those of the Brotherhood itself? Or had a Brotherhood Elder finally exhibited the selfless behavior that should serve as a model for the entire order? Caught in the middle, the ruling Elders made the only decision they could – they would still recognize Elder Lyons as a leader of the Brotherhood of Steel, and the Citadel as their D.C. headquarters. But all material and personnel support from the West Coast was completely cut off. If Lyons wanted to pursue his own agenda on the East Coast, he would do it alone.

So that is what the stalwart Elder did. The Capital Wasteland division of the Brotherhood of Steel, headquartered in the Citadel, became its own entity like the Midwestern Brotherhood of Steel: keep its laws and customs, but no more affiliated with the original Brotherhood of Steel on the West Coast and completely independent.

Outcasts


Most of Elder Lyons’ soldiers supported his dedication to the welfare of the people of the Capital Wasteland, and were proud of their leader’s commitment to honor and heroism. But there were those who voiced their opposition – loudly, and aggressively. They believed that by abandoning the Brotherhood of Steel’s primary mission of acquiring lost technologies, Elder Lyons had abandoned the very values that defined the order itself.

One night, the dissenters (under the leadership of Paladin Casdin) departed from the Citadel, absconding with weapons, power armor, and other pieces of advanced technology and equipment. This was, without question, Owyn Lyons’ darkest hour. He had become a man of compassion and understanding, and could not help but sympathize with those who had left: he had abandoned the Brotherhood’s primary mission. He recognized that, and took full responsibility. Some of the Knights and Paladins who left had been his brothers in arms for years. Together, they had shared victory and loss, pain and elation. But to those soldiers loyal to Elder Lyons, this dereliction of duty and theft of technology was an act of cowardice and treason. Lyons was left with little choice: he branded the dissenters “Outcasts”, traitors to the Brotherhood of Steel – it was a name they would ultimately wear like a badge of honor, proud of the distance it put between themselves and Lyons’ “soldier sycophants”.

Current status
In 2277, Elder Lyons’ daughter Sarah Lyons is now a grown woman, and one of the Brotherhood’s fiercest warriors; in fact, she’s the only member to have achieved the illustrious rank of Sentinel, and now commands her own elite squad, Lyons' Pride.

The war with the super mutants – a conflict that has continued unceasingly for over twenty years since the Brotherhood expeditionary force arrived on the East Coast – rages on, and the Brotherhood is feeling the strain of this extended conflict. Without reinforcements from the West Coast, Lyons has been forced to recruit locally from the wastelander settlements, and the results have been less than stellar: most new recruits are overeager, unskilled, or both, and as a result their survival rate is atrocious. So low, in fact, that word had spread throughout the Capital Wasteland – join the Brotherhood of Steel, and you’ll be dead within the week.

The Brotherhood Outcasts re-dedicated their lives to the Brotherhood of Steel’s original mission – the acquisition and preservation of lost technologies, operating out of the aptly named Fort Independence.

Project Purity, the Enclave, and Broken Steel
When the Brotherhood discovered Project Purity, based inside the Jefferson Memorial, they decided to help defend the scientists that worked on the project from the frequent super mutant attacks. The goal was simple, and beneficial: huge amounts of pure, non-radioactive water for the Capital Wasteland. The only problem was that large-scale tests of the project were always unsuccessful. As time went on, and super mutant attacks became more frequent, the Brotherhood became disinterested with the project. In 2258, Lead Scientist James's wife, Catherine, died in childbirth, and James abandoned the project to find a safe haven for his new child, and the project collapsed. The Brotherhood focused on fighting the super mutant threat for the next two decades, while also attempting to also learn of their source.

In 2272, a man by the name of Three Dog set up a news/music radio station inside the middle of the D.C. ruins, and the Brotherhood struck a deal with him. As stated by Sentinel Lyons "The Brotherhood needed a roof over their heads, and the guy here needed to not get his head blown off. It's a mutually beneficial relationship." The Brotherhood continue to use the GNR building as a "port in the storm".

Eventually, James' child emerges from Vault 101 to find his/her father who wants to restart Project Purity in 2277. A science team is brought together, and repairs are started. Soon though, the Enclave's forces show up, and storm the Purifier. Colonel Autumn demands that the project be handed over to the government, but James adamantly states that Project Purity is private and intended to benefit all the people of the Capital Wasteland. To make a point, Autumn shoots the scientist in the room. James then sacrifices himself by flooding the control room with radiation, and killing himself, along with the Enclave soldiers, but Colonel Autumn survives.

The remaining scientists and the Lone Wanderer manage to go through the old Taft Tunnels that link the Jefferson Memorial to the Citadel at the Pentagon, with only the Lone Wanderer to defend them from any Enclave soldiers, or feral ghouls along the way. When they reach the end, a Brotherhood of Steel member will make a final stand with the Wanderer against a final horde of feral ghouls, and get the scientists topside to safety. Once there Dr. Li demands that Elder Lyons opens the gate to the Citadel and let them in, which he does so promptly.

Once inside, Elder Lyons begins to contemplate the threat the Enclave now poses. The Lone Wanderer is sent to Vault 87 to locate a G.E.C.K. that is necessary to start the Purifier, if nothing else than to keep it away from the Enclave. Meanwhile the Brotherhood gears up for war, modifying their weapons and armor in preparation for fighting the Enclave. Scribe Rothchild teams up with Madison Li on the Liberty Prime robot, and together manage to solve the massive automaton's power problems.

Meanwhile, the Lone Wanderer battles his/her way through the dangerous Vault 87 and obtains the GECK, also learning that Vault 87 is the source of the D.C. super mutants. Unfortunately, he/she is captured by agents of the Enclave, and the GECK is installed in the Purifier. He/She is the transported to Raven Rock, an Enclave command base, and then interrogated by Colonel Autumn for the activation code, but is interrupted by President Eden, who requests a meeting with him/her. Unfortunately, Colonel Autumn soon orders the Enclave soldiers to attack the Lone Wanderer regardless of the president's orders, and the Wanderer must fight his/her way to the president. Once the two finally meet, Eden asks the player to install a modified FEV virus dispenser in the Purifier, as a way to cleanse the Capital Wasteland of all mutations so that only "pure strain" humans like those in the Enclave and the Vaults will survive. The player is forced to leave with the virus in hand, but has a chance to "blow up" Eden and Raven Rock, if he/she wishes to.

Once the Lone Wanderer makes it back to the Citadel, Sentinel Lyons asks her father permission for an assault on the Purifier, which he denies, until the Lone Wanderer tells Elder Lyons of the current situation. Elder Lyons then asks the player for any important information before proceeding. At this point, the player can hand over the Modified FEV (positive karma), tell the Elder about the super mutants and Vault 87 (positive Karma), and about the current status of the Enclave (no karma). Then the Elder asks Rothchild whether or not Liberty Prime is ready to go into battle. Rothchild is skeptical as he'd only just gotten it operational, but ultimately agrees that if it's not yet fully ready then it won't matter in the long run. Sentinel Lyons recruits the Wanderer as an honorary member of the Pride, and together the Pride sets out for the Memorial.

Liberty Prime easily clears the way through all Enclave forces, clearing a path for the Pride. Once inside the Jefferson Memorial, the Wanderer and Sentinel Lyons make their way through the last of the Enclave forces, and eventually confront Colonel Autumn. The Lone Wanderer's can choose the ultimate outcome, but regardless the two make it to the control room whereupon Dr. Li tells them that something has damaged the Purifier, that it must be activated now, and that the current radiation levels would kill whoever enters the room to carry out the activation. The outcome here is also dependent on the choices of the Wanderer, and either someone goes inside to activate the Purifier, only surviving if the Broken Steel add-on is already installed, or no one goes in and everyone within the room dies. Likewise, at this point the Wanderer can secretly use the FEV to poison the water.

With the Purifier up and running, the Brotherhood takes control and begins distributing the clean water throughout the Wasteland with Scribe Bigsley overseeing operations (supposedly to get rid of him). Also during this time, the Brotherhood begins systematically destroying all remaining Enclave outposts in the Wasteland with Liberty Prime spearheading the assault (even destroying Raven Rock if the Wanderer had not done so already). During this time the Brotherhood also begin to reverse-engineer the Enclave's plasma weaponry, removing that advantage for their enemies. Two weeks after the assault on Project Purity, the Lone Wanderer awakens in the Citadel's clinic, and is greeted by Elder Lyons. Scribe Rothchild updates the Lone Wanderer on the current situation on the war between the Brotherhood and the Enclave, then directing the Lone Wanderer to journey to Rockland to help with a Brotherhood attack on an Enclave communications facility.

The Lone Wanderer makes it to the Rockland car tunnels, and assist Paladin Tristan, and a squad of Brotherhood members, and Liberty Prime in the attack. The Enclave forces are decimated, and Liberty Prime manages to literally punch a hole through the Enclave's defenses, giving the Brotherhood an access point. Then, Liberty Prime detects a signal and orders the Brotherhood forces to retreat. Soon after the area is destroyed, along with Liberty Prime, by an orbital bombardment from a weapons satellite ordered by the Enclave, leaving the Brotherhood shaken. Paladin Tristan orders the Lone Wanderer to lead a squad of Brotherhood members to find out what had happened.

At the Citadel, the Brotherhood are really taken aback by the orbital assault. Moments before the attack they had been crushing any Enclave resistance, and now they have lost their biggest weapon, and are facing a new weapon they know nothing about. In addition, it is certain that the Enclave will counter-attack, especially since the Brotherhood was the one to instigate the war. When the Lone Wanderer comes back from the Rockland Satellite Station, he/she delivers some encrypted data for Scribe Rothchild to decrypt, who is aghast at all the hard work that went into restoring Liberty Prime, only to see it all go to waste. Paladin Tristan then sends the Lone Wanderer to the Old Olney Powerworks for a Tesla coil, so the Brotherhood can recreate Liberty Prime's liberty laser, the only effective defense the Brotherhood had against the Enclave's Vertibirds.

The Lone Wanderer does so, with a prototype device made by the Brotherhood meant to jam the signal the Enclave uses to control deathclaws. The Lone Wanderer makes it to Olney Powerworks, encountering many deathclaws, Enclave forces, and robots, but eventually he/she makes it to the center with a functioning Tesla Coil in the middle. With the Tesla coil in hand, the Lone Wanderer makes it back to the Citadel and hands it over to the Brotherhood scientists there, and is then ordered to make it to the Adams Air Force Base via the Presidential Metro. When the Lone Wanderer enters the Air Force Base, he or she opens up a supply crate, containing ammo and a working Tesla cannon. When opening the crate, the Brotherhood receive a signal to commence attacking the Air Force Base, so the Lone Wanderer can make his/her way through the Enclave forces and open the way to the Mobile Base Crawler. Eventually the player makes it to the top of the Mobile Base Crawler, and has a choice to either launch the Enclave's last orbital ballistic payload on either the Mobile Base Crawler, setting back the Enclave in the Capital Wasteland severely, or on the Citadel, thus devastating the Brotherhood of Steel. Once outside, a Brotherhood squad, led by Sarah Lyons if she survived Project Purity, pilots a stolen Vertibird to take The Lone Wanderer back to the Citadel.

By canon, the Lone Wanderer destroys the MBC, and the Enclave is permanently removed as a threat from the Capital Wasteland. The Capital Wasteland Brotherhood moves on back to normal, taking out the mutants and raiders.

With the Brotherhood in control of Project Purity (providing access to clean, purified water), one Vertibird and vast amounts of technology and equipment acquired from the Enclave after the successful war, and access to local recruitment and manpower, the Capital Wasteland Brotherhood is effectively in control of the Capital Wasteland. The original Brotherhood however in California, is more weakened than before by 2281.