A movement of Alphas from all over the country that reject the labels of regular people. Red Flag is referenced in the first episode as a terrorist organization, based in a cell structure. In a message released in the episode Rosetta, the organization believes in "Neurodiversity." This serves as an umbrella term for the neurological disorders and mutations that give Alphas their abilities. So far, the organization has been seen recruiting Alphas and defending against government anti-Alpha policy (in Rosetta, they destroyed the supply of neonatal drug that would prevent someone from being born with Alpha ability). Because of the Alphas who support Red Flag, they are able to remain hidden from government scrutiny.
According to the episode The Unusual Suspects, government involvement in the Alpha phenomenon stretches back to the MK Ultra experiments of the 1960's.
In Rosetta, the team chases Milos Kosar while he attempts to destroy a supply of anti-Alpha neonatal medication. In the process, they find out that omniglot Anna is one of the leaders of the organization.
In Blind Spot, a obstetrician, Dr. Kern (gifted with sonic abilities including echolocation), works on behalf of Red Flag to encourage Alpha-like birth defects in his patients.