A Homonculus is a golem crafted in the form of a magus and capable of using their abilities, though they are incapable of feigning emotion. The base form of a Homonculus is a naked doll with grey hair.
In Rosenkreuzstilette, Homonculi appear in the Iris Palace and take the forms of Spiritia Rosenberg's friends. They were created by Iris Zeppelin to test Spiritia's abilities before confronting her at the ballroom where Iris resides.
There are eight Homonculi that Spiritia must defeat before fighting Iris. Each Homonculus will take the form of one Spiritia's friends whom she fought before entering Count Zeppelin's Castle. The Homonculi can be fought in any order, just like Spiritia's friends beforehand. Once all of the Homonculi have been defeated, a teleporter will appear to take the player to confront Iris.
In Rosenkreuzstilette ~Freudenstachel~, Freudia Neuwahl learns from Sichte Meister that the army of the Orthodox Church has deployed Homunculi modeled after the RKS members. This serves to both wear down the magi and cause in-fighting between them, as shown when Sichte attacks Freudia to prove that Freudia is not a Homonculus.
Freudia later encounters a Homonculus modeled after Liebea Palesch at the end of the White Desert. "Liebea" appears to be emotionless and Freudia suspects something about her to not be right, which she confirms by revealing her true nature upon defeating her. Even with all of her garments ripped off upon defeat, this particular Homonculus retains Liebea's hair and forehead jewelry.
Notable differences from the originals
- Against the Freudia Homonculus, there is less room to avoid her snowflake barrier, but the duration of this attack is shorter than the original.
- Against the Zorne Homonculus, the countdown where both the player and Zorne will be defeated when time runs out will not occur.
- Against the Trauare Homonculus, the Homonculus is fought out of the water.
- Against the Luste and Schwer-Muta Homonculi, the ground is entirely flat.
- Against the Sichte Homonculus, the player can use the walls to evade her attacks in Rosenkreuzstilette ~Grollschwert~ as Grolla.
- Against the Liebea Homonculus in Rosenkreuzstilette, there will not be either of the blocks that collapse beneath the player's weight to the sides of the room.
- The Homonculi are a reference to the Doc Robots from Mega Man 3, as the "spirit" from Spiritia's defeated friends floats down and fuses with the host body.
- Like the re-battle against the Robot Masters in Mega Man 3, most of the Homonculi are also weak against the weapon of the character the assume; the only ones that are not weak against its own weapon are the Freudia and Grolla Homonculi.
- The battle against the Homonculi is a reference the Mega Man series' re-battle against the Robot Masters in the final stages of the game, starting from Mega Man 2.
- The music that plays when the player fights the Homonculi is "Closed Garden", composed by Unlimited Hellest, which is the same music that played during the boss battles against the Webmaster Spider and the Deviled Egg.
- The Liebea Homonculus in Freudenstachel is the only one out of the twelve main bosses, (the eight RKS members and the four Schwarzkreuz members) in Freudenstachel to explode upon defeat in Story Mode instead of teleporting away.