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The original Gammorin and his mutants were pursued by the Brotherhood into the Midwest. Although most of the Brotherhood (in their airships) ended up settling near Chicago, one airship crashed near the Mutants camp.
Paladin Latham survived the crash, and challenged the mutant leader to one on one combat. Latham won the battle, and took over leadership of the horde, and Gammorin's name. After a head injury, he began to see the super mutants as his own people.
The army eventually encountered the robots from Vault 0, and began to fight this threat. Sometime afterwards, Latham realized his purpose and declared himself a mortal enemy to the 'enemy of the west'.
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The Gammorin Army's research into reversing super mutant sterility was destroyed, and their leader perished in battle. Demoralized, the super mutants ceased organized resistance. Some of them tried to escape, others continued to fight. The remaining soldiers were absorbed into the ranks of the Brotherhood of Steel to aid in the war against the Calculator.
The Brotherhood-Gammorin War appears only in Fallout Tactics.