A split soon formed in the Brotherhood, however. One faction supported allowing tribals (human outsiders) to join the organization to prevent a lack of troops. The other faction wanted to keep the Brotherhood pure and not accept outsiders. The faction against expansion won out, and the other faction was sent across the mountains on great airships to destroy the remnants of the mutant army defeated in the first Fallout game. A lightning storm struck down the ships, however, and they were dispersed and forced to crash-land. One of the surviving airships crashed near the ruins of post-war Chicago. After regrouping, and free from the Brotherhood members in California who wanted nothing to do with the tribals, the crash survivors established a first base near Chicago and founded a new Brotherhood that would grow and expand by recruiting outsiders and expanding across the land.
The next challenge in the Brotherhood's campaign are the Beastlords, humans who are able to control the animals of the wastes, and who have come to use Deathclaws as their servants. Once again, the Brotherhood fights the menace, and once again the Brotherhood emerges victorious. Before the Brotherhood can rest, however, they encounter a new foe as they push into post-war Missouri, an area known as "the Belt": the remnants of the mutant army they were sent to destroy. The initial battles are costly to the Brotherhood. Outgunned and outmanned, the Brotherhood is overwhelmed outside of St. Louis. There General Barnaky, head of the Brotherhood, is captured by the Toccomata, leader of the mutant army. Although the Brotherhood is able to withdraw, they remain under constant attack. A squad dispatched to destroy a munitions manufacturing plant instead finds a laboratory dedicated to curing mutant sterility. The Brotherhood claims the lab in order to use it as a future bargaining chip. A few days later, at the ghoul town of Gravestone, in the ruins of Kansas City, Brotherhood scouts find an intact nuclear bomb. The Brotherhood defends the town from several mutant encroachments, and they are soon able to remove the weapon to a safe bunker.
Brotherhood scouting reveals the base of the mutants to be at Osceolla, near the ruins of one of the wrecked Brotherhood zeppelins. A squad fights its way into the base. Inside, they find Toccomata, who is dying. He reveals that General Barnaky had been lost to an unknown menace from the west that was too powerful for even the mutant army. As the squad enters the room where the mutant leader was hiding, they find Paladin Latham, one of the leaders of the Brotherhood air convoy. He tells the squad that after crashing, he fought Gammorin in hand-to-hand combat for leadership of the mutants. Latham won, but a head injury from the battle became infected, and he soon became delusional. Latham assumed the identity of Gamorin, and led his new army against his old allies. The squad kills Latham before he can endanger the Brotherhood even more.
Soon, the menace from the west reveals itself: a robot army is sweeping across the American Midwest. The reavers, a cult dedicated to technology worship, is caught between the Brotherhood and the robots as the two armies clash in Kansas. Although the Reavers try to wage a two-fronted war, they are soon beaten, and seek sanctuary among the Brotherhood in exchange for an electromagnetic pulse weapon. The Brotherhood agrees, and a squad armed with the new technology destroys a robot repair plant as they push into Colorado, towards Vault Zero. It is revealed that the robots are originating from Vault Zero, and are being directed by an enigmatic enemy known as the Calculator. Evidence uncovered by the Brotherhood points to a catastrophic experiment in the Vault that created the Calculator from a fusion of computers and human brains. The robots regroup, but the Brotherhood is able to use the momentum to destroy a robot manufacturing plant. The robots disrupt this plan when they capture Bartholemew Kerr, a merchant who had roamed among the Brotherhood bunkers. If the robots could gain this information from him, they would be able to destroy the Brotherhood. The squad arrives in time, however, and they put an end to the merchant's life. While there, they also discover the body of General Barnaky-with his brain missing.
As the robots press hard, the Brotherhood creates a plan to destroy the robots at their base, Vault Zero, located in Cheyenne Mountain. Using the captured nuclear warhead, the Brotherhood hopes to blast an entrance into the vault. After a tough fight up the slopes of Cheyenne Mountain, a Brotherhood squad places the warhead. The explosion does its job, and two squads enter into the bunker. The power was disabled by the blast, however, one of the squads must find the auxiliary power so the elevators can be used. Meanwhile, the robots are attacking the Brotherhood's bunker. At the vault, the power is soon back on, and the squad proceeds to the bottom level. There they encounter the last of the robot army, led by a cyborg General Barnaky. The General does not attack, however, when he is reminded of his promise to make the world safe for his wife, Maria (the player must have Maria's photo in their inventory for this to occur, or Barnaky will attack). The squad then makes it to the Calculator. After defeating the last robots that guard the bunker and destroying the brains that kept the Calculator alive, the squad is asked by the Calculator to join minds with it in order to end the war and bring peace to the world. The squad is given the choice to either allow the Calculator to self-destruct, sacrifice a member of the squad as a brain donor to repair it, or allow General Barnaky (if he has been kept alive) to become the donor.
See also: FALLOUT: TACTICS CHEATS & WALKTHROUGH