Cell Flaregunners are a special variant of the Cell Foot Soldier that are mainly only encountered in Tactical Locations.
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When the player encounters one they will usually shoot a flare instantly into the sky, As a result it alerts most of the Cell in the Stronghold while also alerting nearby Cell Road Patrol units in the area arriving outside or inside in any Cell Modified vehicles. Taking them one out like the Director says makes it more easier and less annoying for the Agents, But this can take practice and speed in order to achieve this.