Samus Aran is sent to another nameless planet after the events on Planet Aether. What was supposed to be a routine recon mission turns deadlier when she finds herself embroiled in a war on multiple fronts, especially one in particular: her own mind.
Two and a half years after Samus' successful mission to Equis, the Hunter is reunited with her companions. The circumstances of their reunion, and what they find hidden on the planet, threaten the very place that she now calls home...
Ridley, the dreaded leader of the Space Pirates, was finally put rest after his battle with Samus Aran, on planet Zebes, but after being cloned on the B.O.T.T.L.E ship, a reject clone was sent in a pod to a far off planet, Equestria.
A meteor impacts the nation of Equestria, Planet Equis. Tranquility is quickly snuffed out when a poison begins to spread violently. The Princesses cannot combat this unknown threat, as no knowledge of it exists. Help comes from an unexpected source.