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- Averted in The Mission: Father Gabriel is a benevolent Jesuit missionary, and the evil role goes to Captain Mendoza (pre-Heel–Face Turn).
- A few of the Jesuits in Black Robe, a film set in colonial New France, are pretty unscrupulous — notably, one lies to the Huron and tells them that baptism will cure their smallpox — and the film is certainly critical of the Jesuits' mission, though the film's protagonist is a genuinely good Jesuit who honestly believes he is helping people. His Algonquin guides, however, are pretty wary of him, since he wears the eponymous black robe, sleeps separately from everyone else, and refuses to have sex with the women.
- In Jeff Long's The Descent, the leader of the Hadals, and the inspiration for Satan, posed as a Jesuit, though this was later retconned, changing him to be a mere disciple of Satan (who occasionally is more evil than Satan himself), since he has real human vileness in him, while Satan is just an example of alien Blue and Orange Morality.
- The Victorian historical novel Henry Esmond has Father Holt, who gets involved in the Jacobite Rebellion, and at one point is shown in Germany commanding Catholic military forces under the name "Holtz". More "evil" because he's Catholic than because of anything the character actually does, he's more like a Poisonous Friend to the hero than an actual villain.
- Neal Stephenson's The Baroque Cycle has the definitely evil Edouard de Gex who eventually disguises himself as a Jansenist (a sect which were enemies of Jesuits) and calls himself de Ath.
- Subverting the trope, there is Father Gabriel Goto, a katana-wielding samurai Jesuit from Manila (long story).
- Cunegonde's brother would count in Candide (which was a definite influence on Henry Esmond above) — while a lot of the characters change identities in the book, he becomes a Jesuit but is also at some points a military leader (not surprisingly, as he was written as a Take That against Frederick the Great).
- Ian Pears' novel An Instance of the Fingerpost has one of the unreliable narrators slides between this and Anti-Villain.
- The Wandering Jew has evil Jesuits trying to gain control of the wealth of the title character's last descendants. In a particularly nasty Take That!, a Thugee assassin decides that his Kali-worship is completely compatible with their brand of Catholicism.
- In the sequels to The Three Musketeers, Aramis becomes a Jesuit priest (and later vicar-general of the order) and turns into a Manipulative Bastard, often working against his former comrades-in-arms.
- Stendhal's novel The Red and the Black has the main character (a Byronic Hero) joining unsympathetically-presented Jesuits in his quest for self-advancement and the novel discusses the Jesuit-Jansenist rivalry (which apparently persisted at least into the mid 1800s, when the novel was written/set). The Jesuits aren't presented as that smart though, as the author's Take That! is to present them as close-minded ultra-reactionaries. However, the main character fits the trope, as he is able to fit in just as well among a military-minded aristocratic culture (the red) as among the Jesuits (the black).
- The Swedish-Finnish series of historical novels, The Surgeon's Stories, by Zachary Topelius, has (in the first part The King's Ring which is set during the Thirty Years' War) the character of Father Hieronymus, who is a very stereotypical instance of the trope. He carries a dagger concealed in his crucifix and tries to murder king Gustavus Adolphus, recruiting the young noblewoman Lady Regina (whom he serves as confessor for) to aid him.
- In Flann O'Brien's (author of The Third Policeman) later novel The Hard Life, the protagonist's guardian Mr. Collopy is friends with a Jesuit priest, Father Kurt Fahrt. When Fahrt refuses to countenance Collopy's plan to blow up Dublin City Hall (in a planning dispute over ladies' public toilets), Collopy reminds Fahrt of the Jesuits' own role in the Gunpowder Plot of 1605. He also seems to think the Jesuits were responsible for the Franco-Prussian War.
- Averted in the 1632 series. While one book had a bigoted Jesuit character, he was no more bigoted than any 17th-century person. In fact, a number of the allies of the protagonist uptimers — Americans sent back in time by Alien Space Bats (long story) — are worse. Also, the historical domain characters of Father Friedrich Spee von Langenfeld and Father-General Mutio Vitelleschi are their allies, who are described as good but flawed (as are many characters, protagonist or antagonist). After the Spanish Cardinal Borga usurps Pope Urban VIII, tries to murder him, and murders several of his allies, the Jesuits begin to suffer a schism — one remains loyal to to Urban VIII and thus remain friendly to the uptimers, while the other — mostly composed of Spanish Inquisitors and witch-hunters — become outright hostile.
- Averted in Robert Anton Wilson's Historical Illuminatus Chronicles, which feature Father Ratti, a good Jesuit whose open-mindedness contrasts the fundamentalistic Dominicans. On the other hand the books also mention, though never shown (due to Author Existence Failure), Adam Weishaupt, the former Jesuit who went on to found the Bavarian Illuminati.
- Despite portraying some of the worst excesses of the Roman Catholic Church in his novels, Jose Rizal averts this trope, since some of his more sympathetic clergymen characters are Jesuits — in Real Life, Rizal was very fond of his Jesuit mentors.
- Mentioned in British statesman Lord Chesterfield's Letters to His Son. "I do not know a crime in the world, which is not by the casuists among the Jesuits (especially the twenty-four collected, I think, by Escobar) allowed, in some, or many cases, not to be criminal." (letter 52) Although he regarded the Jesuits as the "most able and best governed society in the world." (letter 85)
- The Confessor, a telepathic serial killer from the Global Guardians PBEM Universe was a Jesuit priest before gaining his powers, which let him see just how wicked human beings could be.
- The "Black Pope" is a derogatory term coined in Protestant European politics during the 16th century referring to the Superior General of the Society of Jesus. Often considered irredeemably evil by those who coined the term in the first place, the "Black Popes" were only as bad as their very human failings. A number were decent people overall, and were even, for their time, pretty much liberal-leaning.
- The Jesuits' philosophy of casuistry (case-based reasoning) came in for much criticism in its time, including by Catholics like the French philosopher Blaise Pascal (a Jansenist). In particular, they were attacked for arguing that deception (especially under oath) was not always wrong if it saved a life. This resulted from the cases of captured Jesuit missionaries who were forcibly sworn to tell the truth in court by Protestant authorities and then ordered to identify people who had harbored them-knowing that any person named would be put to death, as this was a capital crime. Thomas Sanchez, a famous Jesuit, therefore formulated the doctrine of mental reservation. In its strictest form, the person practicing this might answer "I know not" when asked a question, while internally they said "to tell you." Other philosophers did not accept that it was anything but simple lying. This doctrine was eventually condemned by the Pope after it had become scandalous, and tarred the Jesuits' reputation. Critics such as Pascal also ignored the restrictions Sanchez had placed on its use, attacking a strawman version of it. The wider form of mental reservation, equivocating between words' meanings (for instance answering "I am not a priest" while thinking about some other priest), was still viewed as orthodox afterward. A similar form was saying misleading but technically true things, Catholic saints such as Athanasius of Alexandria having used it to save their lives: Athanasius' followers, according to legend, were asked by Roman soldiers pursuing him who did not know his appearance if they had seen him and they replied "Yes, he is not very far off" when he was in their company at the time.