The agents of HARMOMY, led by The Boss, has betrayed Twilight Sparkle and The Equestrian CIA.

The EIA is a crime organization, and a rather special one in fact. Recently, they came into power over a country that's not recognized by the Council of International Affairs up until now; they are now a terrorist organization with the, supposedly, capacity of becoming the most Nuclear-powered militant Equestria has ever seen.

Twilight Sparkle, codenamed "Sparkle Snake", was The Boss's apprentice for many years. After The Boss's disappearence and Luna's position on the throne, Twilight Sparkle retired. The Agency HARMONY, now ran by Luna, contacts her with an imperative mission. However reluctant she is to come out of retirement, the Equestrian CIA needs her to locate the nuclear threat and comfirm EIA's weapon 'To Surpass Metal Gear' is real and it's location through the weapons scientist by the name of "808.808".