The story takes place in Manehatten where a mutated version of Cutie Pox known as Bit Poison has devastated the government of Equestria. The Strategic Homeland Division is activated to save what remains and preserve the government. They are sent to Manehatten to help liberate the city from three hostile factions. The Ravagers, The Followers, and the Wolf Private Army.

The main character is Shadow Dawn. A bat pony activated in the second wave. But she will work together with three other agents. Autumn Rush, Cloud Dancer, and Rain Rider. While trying to liberate the city. Shadow Dawn will also try to piece together what happened to the first wave of Division agents.