After an Adeptus Mechanicus Explorator vessel discovers Equestria whilst mapping unexplored parts of the Segmentum Obscurus region of the galaxy, a series of events leads it to become allied with the Imperium of Man because of its inhabitants' unique properties, which include protection from the Warp's corrupting influence and potent psyker abilities amongst approximately a third of the population. After Princess Celestia manages to prevent Equestria's destruction through mysterious means, unicorns are recruited to serve in special units to fight the forces of Chaos. This story follows a pair of young unicorns that serve in one of these units as a fourteenth Black Crusade develops.
(Not adherent to a significant portion of Wh40K canon. Warhammer 40,000 and related materials are property of Games Workshop.)