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The Resistance Army is the main army that Byleth commands in the Silver Snow route, which occurs if Byleth decides to oppose Edelgard in the Holy Tomb. Alternatively, if the conditions to unlock Edelgard's Crimson Flower route are not met, the game will default to the Silver Snow route with the Church. Awakening from a five-year coma, Byleth meets Edelgard in the ruins of Garreg Mach. Unable to accept the depths Edelgard has fallen to achieve her goals, Byleth clashes with her one final time before they part ways. After reuniting with Seteth and the students of the Black Eagles, they clear out bandits from the monastery and make it their base of operations. Afterwards, Seteth declares Byleth's army as the Resistance Army, and creates a flag based on the Crest of Flames as its motto.
- Byleth Eisner - The former professor of the Black Eagles House at Garreg Mach Monastery and commander of the Resistance Army.
- Ferdinand von Aegir - The competitive and industrious former heir to House Aegir before his father Duke Aegir was stripped from his belongings. He joins the Resistance Army in hopes of striking down the Empire and regaining what he had lost.
- Linhardt von Hevring - The carefree heir of House Hevring who goes out of his way to shirk responsibility. Has a keen interest in the nature of Crests.
- Caspar von Bergliez - The second son of House Bergliez. Not expecting an inheritance, he leaves his family and plans to make a name for himself in the Resistance Army.
- Bernadetta von Varley - The shy and withdrawn daughter of Count Varley. With the Count under house arrest, she finds home in the Resistance Army.
- Dorothea Arnault - One of the few commoners among the ranks, she was a former songstress for the Mittelfrank Opera Company.
- Petra Macneary - Princess of Brigid who wishes to give her kingdom independence from the Adrestian Empire.
- Seteth - The missing archbishop's assistant and second-in-command of the Resistance Army.
- Flayn - A gentle and gregarious girl who wishes to end the conflict between the Church of Seiros and the Empire. She is also Seteth's younger sister.
- Catherine - A member of the Knights of Seiros and former outlaw from the Holy Kingdom of Faerghus, Catherine only wishes to rescue Rhea and stop the Empire.
- Shamir Nevrand - A member of the Knights of Seiros that was taken in by Rhea and wishes to repay her debt.
- Cyril - An Almyran war orphan taken in by Rhea and trained as Shamir's apprentice to repay the archbishop for her actions.
Any students and/or staff members from Garreg Mach that Byleth has successfully recruited are also among the ranks of the Resistance Army. The exceptions are Ashe and Lorenz, who do not make it to the promised meeting five years later. Both are encountered as enemies in later battles, who can be recruited again if they previously joined the Black Eagles house, are defeated, and spared. Hilda is only recruitable in the final month of the Academy Arc of Silver Snow.
- Felix Hugo Fraldarius
- Sylvain Jose Gautier
- Mercedes von Martritz
- Annette Fantine Dominic
- Ingrid Brandl Galatea
- Raphael Kirsten
- Ignatz Victor
- Lysithea von Ordelia
- Marianne von Edmund
- Hilda Valentine Goneril
- Leonie Pinelli
- Hanneman von Essar
- Manuela Casagranda
- Alois Rangeld
- Yuri Leclerc
- Balthus von Albrecht
- Constance von Nuvelle