The Flame Emperor Army is a militant faction led by the Flame Emperor and their lieutenant, the Death Knight in Fire Emblem: Three Houses. The objectives of the Flame Emperor Army are unknown, but it seemingly opposes the Church of Seiros and is also in a strained alliance with Those Who Slither in the Dark.
In Imperial Year 1180, the Flame Emperor sent Kostas and his band to attack Edelgard, Dimitri, and Claude, three students of Garreg Mach Monastery's Officers Academy who were the heirs of their respective countries, while they were on a camping trip. The students were saved thanks to the timely intervention of Byleth and Jeralt, and later Byleth was revealed to have a mysterious power: the Crest of Flames.
The Flame Emperor was intrigued by this development and decided to monitor Byleth's activities. They orchestrated an attempt by the Western Church to steal the Sword of the Creator; this was thwarted by Byleth, and Archbishop Rhea gave the sword to Byleth.
The Death Knight next led the Flame Emperor army to abduct Flayn on behalf of Solon, a mage working for those who slither in the dark; after being defeated, the Flame Emperor appeared before Byleth for the first time before fleeing with the Death Knight.
Two months later, during the massacre at Remire, Flame Emperor soldiers commanded by the Death Knight aided Solon in battle, but were again driven off. In the aftermath, the Flame Emperor appeared again to plead ignorance of the massacre and disavow Solon's actions. The Flame Emperor attempted to recruit Byleth and their father Jeralt, to no avail.
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The final appearance of the Flame Emperor army was an invasion of the Holy Tomb to steal the Crest Stones that lay within. Over the course of this battle, it was revealed that the Flame Emperor Army was in truth an Adrestian black ops group commanded by none other than Princess Edelgard von Hresvelg, in her crusade to destroy the Church of Seiros out of the belief that they were directly responsible for the stagnation of Fódlan.
The Flame Emperor Army was ultimately absorbed into the greater Adrestian military, and Edelgard's personal bodyguards were reorganized into the Supreme Armored Co.