General Simon Barnaky was the commanding officer of the Midwestern Brotherhood of Steel from 2197 until 2198. He, as 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 adviser, 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.
"While most of our Elders believe ghouls are almost our equals, I do not agree."
"I pray the Brotherhood can remain pure at heart with this foul taint" - referring to ghouls joining the Brotherhood.
"Science and discipline will always be victorious over ungodly mutation."
"Between you and me, Brother, sometimes I wonder if the old Elders were right."
"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."
"You cannot stop the future, just as you can't stop the rain from reaching the ground."