Barbatos Goetia was a former member of the Er'ther Army, who sold out his people to the Aetherians during the Aeth'er Wars so that he could be on the winning side. Due to the scale of the atrocities he committed, Barbatos's name was removed from history altogether. Following his resurrection by Elraine, Barbatos acts as her personal assassin, going after the heroes who saved the world from the resurrection of the Aethersphere and the superweapon Belcrant. In order to kill two of these heroes, Stahn and Rutee, Babartos uses a little boy as a hostage and threatens to kill him unless they drop their weapons. After they do so, Barbatos kills Stahn and cripples Rutee. Barbatos then tries to kill High Priestess Philia Felice and King Garr Kelvin of Phandaria, the latter of which he attempts to kill after crashing an airship into the royal castle as a distraction. When he returns with Elraine to the past, Barbatos encounters Dymlos, the old enemy who had killed him, and, in revenge, kidnaps a girl who's in love with Dymlos to use her as a hostage to force the weakened Dymlos to duel him. Utterly self-centered, Barbatos's ultimate goal and obsession is to force history to recognize him as a hero, even as he commits every evil deed imaginable and has no comprehension of what true heroism is.
Kvar is a Mad Scientist infamous for being the cruelest of the Desian Grand Cardinals. Heartless and sadistic, Kvar runs a Human Ranch where his prisoners are turned into Exospheres in a process that leaves the party horrified. Discovering that some of his prisoners escaped from the ranch to the village of Luin, Kvar attacks Luin, destroying the village, killing many and capturing the survivors for his experiments. When Lloyd encounters Kvar, the Cardinal brags about how he removed the Exosphere from Lloyd's mother, causing her to turn into a monster and attack both her child and her lover, Kratos, which resulted in Kratos killing her to save their son. The depth of Kvar's depravity is such that even his own men are appalled by him.
Rodyle is another Desian Grand Cardinal who shares Kvar's penchant for mad science. Taking over Kvar's experiments following his death, Rodyle manages his own Human Ranches and is working to create a superweapon, the Mana Cannon, in order to destroy the Tower of Salvation, overthrow his boss, and become the ruler of two worlds. When the party frees the Ranch's prisoners, Rodyle manages to trap the prisoners again and floods the room they're in, forcing the party to watch. Following his defeat, Rodyle activates the self-destruct sequence of his Human Ranch to make sure the heroes and everyone else in the Ranch dies with him.
Zilva Madigan is the genocidal leader of the Four Stars and the one pulling the strings behind the Kingdom of Callegea to ensure that the Gajuma reign supreme and the Huma are all eradicated. To achieve this, Zilva possessed the body of Dr. Barrs, the most revered doctor in the kingdom, then used it to poison and kill Ladras Lindblum, the King of Karegia. Following this, Zilva used Dr. Barrs's body to attack his good friend, Eugene, forcing Eugene to kill Barrs in self-defense. This led to Eugene's exile for "murder." Afterwards, Zilva began manipulating the naïve daughter of King Ladras, the new queen, Agarte. Zilva convinced Agarte to kidnap beautiful Huma girls for Agarte to switch bodies with, kick starting the events of the game, and later convinced Agarte to revive Geyorkias, the King of Sacred Beasts. This was all done so that Zilva could take over Callegea and use Geyorkias's power to cleanse the world of Huma. Unlike most other villains in the series, Zilva has no Freudian Excuse for her crimes, she's just a cruel Fantastic Racist who believes the Gajuma are superior, and deserve to rule.
Vaclav Bolud is the Evil Prince of the Crusand Empire whose ultimate goal is to conquer the world. Vaclav first sends out Senel Coolidge to capture the Merines that control Legacy, a small continent that acts as a ship, in order to seize Legacy for himself. When Senel befriends the Merines instead of capturing them, Vaclav launches an allout assault on the Village of the Ferines. Though Vaclav doesn’t capture his targets, he does kill many of the Ferines and kidnaps Stella Telmes, the Merines sister, because he views her as useful. Trapping her in suspended animation, Vaclav turned Stella into a proto-Merines and used her to control the Legacy, with the ultimate goal of using Legacy’s Nerifes Cannon to destroy the Holy Rexalian Empire. Vaclav also committed genocide against the Orerines people and performed vicious experiments on them in special camps.
Cumore, a captain of the Imperial Knights, is from a noble family and considers peasants to be completely beneath him. When he is placed in charge of the town of Heliord, he tricks peasants into volunteering for brutal labor with the promise of making them nobles. Cumore has no authority to ennoble people and he knows it. The labor these peasants undergo is so brutal that many of them die of exhaustion. Later, Cumore is sent to govern an oasis town to find a monster that lives in the desert. While in this position, he forces the peasants in the town to go into the desert to find the monster, knowing that this will likely kill them. The only remorse Cumore shows for his crimes is that they eventually lead a vigilante to kill him.
Ragou is the corrupt magistrate of Nor Harbor. Nor Harbor has been experiencing storms, making it hard for the people there to make a living off of the port commerce. To make things worse, Ragou harshly taxes his people. If someone cannot afford his taxes, Ragou sends his mercenaries to take their loved ones (including children) as collateral. He keeps these loved ones in a basement full of monsters. When the heroes confront him over this, he explains that he finds people getting eaten by monsters to be entertaining. Ragou offers only one hope to his people: if they kill a vicious monster and bring back its horn as proof, they will never have to pay taxes again. Of course, this monster would make short work of most people who try to fight it. The heroes eventually discover that the storms around Nor Harbor are created by a special Blastia in Ragou's mansion. He orchestrated the suffering of his people for his own amusement.
Alexei is the Commandant of the Imperial Knights. However, he betrays his Empire in an attempt to conquer the world. To accomplish this, Alexei orchestrates a genocide of the Entelexeia, the race that protects the world, so he can harvest the powerful apatheia from their corpses. Two of his minions are forced to obey him because he will shut off their artificial hearts at the first sign of defiance. He tortures Estelle, a member of the royal family he was sworn to serve, to force her to use her powers to activate Zaude, an ancient superweapon. Using Estelle for this purpose floods Zaphias, the capital city of the Empire, with deadly aer and vicious monsters.