The Ghouls of Quincy are overjoyed by your dedication to protect them along with their human counterparts. As a result, there are now ghouls applying for membership into the Brotherhood. The Elders believe that their inherent resistance to certain toxins makes up for their sub-human frailties. I pray the Brotherhood can remain pure at heart with this foul taint.
General Simon Barnaky was the commanding officer of the Midwestern Brotherhood of Steel from 2197 until 2198. He was one of the original young paladins who disagreed with the Brotherhood's code and rebelled. He wanted to bring technology to the outside world, just not to every wastelander. Barnaky was also the squad leader of the elite Brimstone Squad.
Simon Barnaky was a part of the minority within the Old Brotherhood that wanted changes to policies, including the sharing of technology and knowledge with outsiders and letting in wastelanders. He believed that the Brotherhood of Steel had much to offer humanity, no matter how primitive. The Whachutu of Peoria are a prime example. However, Barnaky was bigoted towards mutants and believed they deserved nothing but scorn. When the Elders started to include mutants into the Brotherhood, Barnaky openly spoke out against it. He questioned the wisdom in such an act, voicing his belief that mutations would taint the Brotherhood and questioned if the Old Elders were right. He was not alone in this view; the Elders themselves didn’t believe that mutants were truly the equal to pure blood humans, but they felt they could contribute in other ways.
General Simon Barnaky had a wife named Maria. He dedicated his life to her, and vowed to cleanse the land of impure mutations and monsters to allow normal humans to thrive.
In 2198, Barnaky was taken prisoner by Gammorin's Army in St. Louis. This same convoy, with the captured general, was then intercepted by the Calculator's robots and Barnaky was taken to Scott City. There, after extensive torture and experimentation, General Barnaky's brain was extracted and put into a robotic suit. The Calculator's plan was that Barnaky's knowledge about the Midwestern Brotherhood's internal and external workings could be used to facilitate many of the Calculator's further objectives.
Simon Barnaky, now as a humanoid brain bot with a semi-lobotomized brain and robotic programming, saw the power of the Calculator as humanity's last chance to bring a new order to the wastes. There was now a possibility to offer humanity a world of order and peace, a world free of war, free of mutants and chaos. The brain bot form of Barnaky ignored the fact that the Calculator was corrupted and sought to exterminate all life. Barnaky knew only that his "pacification protocol" was able to bring death to mutant abominations. He successfully retained a part of his consciousness along with new programming without conflict between them. After that, he had become the Calculator's right-hand. He was a protector and advisor, an enemy and betrayer to his old comrades, whom he believed to be corrupted by genetic mutation. He tried to use his former position as a leader of the Midwestern Brotherhood of Steel to serve the Calculator's army by effectively erasing defensive measures of the Midwestern Brotherhood.
Faced with Simon Barnaky being listed as missing in action, the rank and position of General/commanding officer of the Midwestern Brotherhood of Steel was given by the elders to Dekker.
While Simon Barnaky's brainless body was discovered in Scott City, the truth about his alliance with the Calculator was only revealed in Vault 0, where the Warrior encountered brain bot Barnaky guarding the Calculator. Barnaky was very confident in his master's goals, believing the Calculator's way to be the best for the wasteland.
There are three possible ways the general's story could end, depending on how the Warrior chooses to deal with him:
He could come back to his senses after the Warrior reminds him of his wife using his locket or his holotape. In this case Barnaky would become ashamed of his betrayal, his new form and the prospect of human extermination. After this, the Warrior could put Barnaky's brain into the Calculator, which would then take on a pro-Prime human mentality and begin to restore mankind to its prior glory at the cost of all mutated beings and mariposa super mutants being hunted down and chased back to the West Coast.
He could finally be killed while fighting the Warrior.
His fate if the Warrior saved him then decided to sacrifice himself to become one with the Calculator is not known. It could be assumed he either becomes the guardian of the Warrior/Calculator, or is executed by the Midwestern Brotherhood of Steel.
"The Ghouls of Quincy are overjoyed by your dedication to protect them along with their human counterparts. As a result, there are now ghouls applying for membership into the Brotherhood. The Elders believe that their inherent resistance to certain toxins makes up for their sub-human frailties. I pray the Brotherhood can remain pure at heart with this foul taint." – After saving the ghouls in Quincy
"The Beastlords have been eliminated and the monsters are no longer under their control. News of our victory has already reached the surrounding towns. The Brotherhood's reputation alone will now have new recruits flocking to our front door. Our scribes were correct on the Beastlords' relationship with their animal lackeys. The Beastlords inherent telepathic suggestion is a unique ability. It is acquired through prolonged exposure to an unknown radiation present within Mardin's underground caves. Unfortunately, we will not be able to duplicate this feat. The scribes explained that this unique mutation only manifests in humans that have been exposed for at least twenty years. But, it is of little matter, since science and discipline will always be victorious over ungodly mutation." – After defeating the Beastlords at Mardin
"These are strange times, warrior. The Deathclaw Matriarch spoke to our Elders today. It seems that her gratitude is genuine and that she is allowing some of her spawn to remain behind when her brood moves on. These Deathclaw young are to be treated as honorary initiates to the Order. Plans are already underway to create a special unit to help assimilate these unusual recruits into our ranks. Personally, I have my misgivings towards these dangerous creatures. I do not believe they should be allowed to fight beside our Paladins. However, the Elders insist on this. Between you and me, Brother, sometimes I wonder if the old Elders were right." – After Mardin mission
"Brotherhood Intelligence has recently uncovered a plot involving the town of Springfield. The plot rotates around Springfield's Mayor Avellone. Intelligence reports that the mayor's political stance with the ghouls has angered some of Springfield's far-right, human activists who refuse to acknowledge the sub-humans as near equals. While I have to say I agree with them... our Elders think otherwise. Dagger Squad already captured one of the ringleaders to this plot, but it might already be too late. Our interrogators have informed me that these resident troublemakers will be dressed as raiders, which is probably a clumsy attempt to frame the local bandits. Normally, the Brotherhood doesn't meddle in politics, but this offers a chance to increase our hold on this resource rich province. Your mission is to find Mayor Avellone and to protect him at all costs. If he is already in the clutches of the kidnappers, you must rescue him and eliminate the one responsible." – After the Springfield mission
"That's far enough, Warrior! Can you recognize me now, even in my new form? You've come along way since my departure, but you haven't come far enough. The Brotherhood has caused many setbacks for us recently, but that's all they are... just setbacks. You cannot stop the future, just as you can't stop falling rain from reaching the ground. The Calculator offers humanity a world of order and peace, a world free of war, of mutants, and chaos. The Brotherhood would be wise to realize that their cause has been tainted by misdirection and genetic mutation, but they can still save themselves if they stop trying to prevent the unavoidable. However, you are too close to my new master and salvation, to be allowed to continue. I salute you warrior, but this is where your mission ends..." – Confrontation in the Calculator's Lair