Following on the events of Valis III, Yūko has become the goddess of the world of Vecanti and has watched over the world in peace since the death of Glames. Trouble brews, however, when a prince of Vecanti named Galgear begins to search for a magical ring. This ring increases his powers, but to the loss of control he could have maintained under its effects, and the gods of Vecanti recognize this and enslave the reckless prince inside a crystal, its mass sinking into the ocean. Fifteen years pass, and Galgear manages to break out of his prison, kidnapping the former heroine Valna and being pursued by troops led by Cham as a result. A member of her band, named Rena Brant, requests permission to infiltrate Galgear's stronghold and free Valna on her own; Cham initially disagrees, but a disembodied voice convinces her to allow this, and Rena brings her twin sister Amu with her. They both succeed in reaching Galgear's inner sanctum, but are stopped by the prince and his ring, who is about to obliterate them when they are teleported away by a magic force—that of Asfer, the prince's father, who tells them that only the Valis sword, no longer in this world, can stop him. Both girls journey day and night to reach the heavens of Vecanti and claim the sword, which is bequeathed onto them by Yūko herself, sent with her blessings in stopping the power-hungry prince. They return to Vecanti and use the mystic blade to defeat Galgear.

Similar to the adaptation of the PC Engine game Akumajou Dracula X: Chi no Rondo into the Super Nintendo Entertainment System title Castlevania: Dracula X , extensive edits were made to Valis IV when it was ported to the Super Nintendo. The playable characters from the original (Asfar, Amu, and Rena) were left to just one (Rena). Also removed were the animated sequences from the original version. Though several levels were removed, a new level (Castle Vanity) was designed for this version.