Fire Emblem: Monsho no Nazo (or "Mystery of the Emblem") is the third game in the series, third released only in Japan, and the first on the Super Famicon. It was divided into two parts, Book One and Book Two.

Book One was a remake of Ankoku Ryu to Hikari no Tsurugi, but featured better graphics (of course, still not Shadow Dragon that we see today.)

Book Two was the sequel to the events of Book One, as Marth rules Altea as king. But when Emperor Hardin of Akaneia begins conquering the other kingdoms, he leaves his rule behind and goes to investigate. He finally discovers that Garnef (Gharnef) has possessed Hardin and all but destroyed his soul, that Medeus has been revived, and the Fire Emblem has lost most of its power. He also finds out that Hardin has taken Altea in his absence. He goes across the continent to find the 12 Star orb shards in order to revive the Fire Emblem, turning it into the Shield of Seals (not to be confused or related to Roy's Sword of Seals). He frees Hardin, but does so by killing him. Hardin thanks him for freeing his soul just before he dies, and Marth revives the Shield of Seals, then going to defeat the newborn Medeus.