Shadow Mitsuo has skills called Whisper, Prayer, and Chant. In Japanese, these skills are named ささやき, いのり, and えいしょう, and are references to a message that appears in Wizardry when you revive dead characters or cure paralysis at the Temple of Cant.[1]
When Shadow Mitsuo transforms into Mitsuo the Hero, his third command is Spell which casts Gigadyne. Gigadyne is a reference to Kazap (Japanese: ギガデイン, Hepburn: Gigadein) from Dragon Quest.[2]
In order to fight Shadow Mitsuo, the Investigation Team must find the Orb of Darkness (Japanese: くらやみのたま, Hepburn: Kurayami no tama). This is a reference to the Sphere of Light (Japanese: ひかりのたま, Hepburn: Hikari no tama) from Dragon Quest.[3]
When the protagonist interacts with the pile of bones to get the Gaia Sword, a message appears that says, "No response. It must be a tile, not an object." (Japanese: 返事がない。ただの飾りのようだ…) This is a reference to how in Dragon Quest, when the hero interacts with a pile of bones or a dead person, a message appears that says, "There's no response. It's just a corpse." (Japanese: 返事がない。ただのしかばねのようだ。)