Millenia of peace dominated by Friendship and Harmony now threatened. What began as huge meteorite that costed Celestia's life to destroy, its remained crumbles that descended upon lands spread toxic and vile crystals that later were deemed Tiberium. Tiberium offered great power and monetary gain, and as such mega-industrialization begun. But it sparked unspoken evil in everybody on the planet, and killing begun. Two main factions arose: Global Defense Initiative (GDI) and Brotherhood of Nod.

The story follows Twilight's experiences with Tiberium and everything relating to it; her bouncing trust with Luna of GDI and Kane Hooves of Nod, her own conflict with oneself and crimes she did. Betrayal, hurt, loneliness, hate, power, destruction and malice becomes her second nature, as Tiberium corrupts her and everything around.