You can't believe everything you see, or can't see, for that matter. In Musaigen no Phantom World, Phantoms, beings that blur the line between illusion and reality, wander around right under the noses of unsuspecting humans. Their origins are mysterious and few can see themーthat is, until a research facility bombing spreads a virus that grants the ability to. Humans with special powers are given the task of sealing the troublemaking Phantoms.

Haruhiko Ichijou is one such Phantom Hunter. Not a very good one, however. Possessing a wealth of useless knowledge, a tendency to go off on tangents, and a rather slow Phantom-sealing ability, he and his rambunctious teammate Mai Kawakami are at the bottom of the Phantom Hunter ladder at Hosea Academy. In order to become stronger, they recruit new teammates and develop new powers, only to stumble upon secrets surrounding Phantoms and the circumstances surrounding the mysterious bombing of the Alayashiki Research Facility.