An Ultimate Rune is the final attack of a boss. Ultimate Runes tend to be stronger than every other Rune used by the boss.
Komakani ~ Wailing Tides ~ Fury of the Seven Seas
Hotaru ~ Vim of the Swarm ~ Piercing Mandibles
Yuzuki ~ Grave Sign ~ Stifling Masonry
Tokokujo ~ Tormenting Heat ~ Fury of the Dragon
Kyra ~ Prevalence of the Cosmos ~ Fury of the Cosmos