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In Mysterious Ways

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God (or suitable equivalent thereof) works in mysterious ways. How mysterious? Really mysterious. Like, chaos theory mysterious. Who knew that ending a war could be as easy as helping one little old lady cross the street — or letting the Girl of the Week get run over by a truck?
In Mysterious Ways is what happens when the divine interacts with the mundane in ways that don't make sense at first appearance. In time, however, the results are palpable. This is usually done to convey a sense of omniscience; after all, if you can see how all events play out, it's more likely you'd go the subtle route than try to rain fire from Heaven every time things don't go your way.
Characters who fall under this trope are unlikely to use an Omniscient Morality License; why put the hero through hell when you can save the day by moving a book across the room? Unless that was the only way they could grow as a person...
If God Is Inept or merely Flawed, He might try to claim "I Meant to Do That!" by invoking this trope.
Implies Butterfly of Doom. Usually overlaps with Gambit Roulette, which is about plans relying on seemingly chance events in general. Compare Maybe Magic, Maybe Mundane and Butterfly of Doom. Often used as flimsy justification for Deus ex Machina and A Wizard Did It. Contrast Divine Intervention, when it's very obvious that the deity was taking action. Compare and contrast Answer to Prayers, when the deity gets involved because their followers asked; it's an open question how clear their involvement will be.
Not to be confused with the U2 song "Mysterious Ways" (that would be God-Is-Love Songs).

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Preacher (2016): In "Gonna Hurt", God tries to convince Tulip that his bizarre behavior and everything that's gone wrong in her life is All According to Plan, but Tulip ain't buying it. "I think you're just screwing around."
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In Castlevania: Lords of Shadow, it is heavily implied that God abandoned Gabriel Belmont, allowing his fate and not letting him be forgiven for his transgressions. However, He is revealed to have a far greater plan one thousand years later, as Gabriel's fall from grace allowed him to have an agent capable of killing Satan once and for all when he brought about the Apocalypse.
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Worm:
This is the Simurgh's preferred method of affecting the world. She subtly influences people en masse so that days, months, or even years later they will make a decision that furthers her agenda. Quarantines are established to keep her victims from doing so, but even that can work towards her plan.
Contessa's power allows her to devise a plan that will allow success for any given task by following certain steps, often seemingly unrelated to the task at hand.
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Occasionally discussed in The Salvation War, with some of the more optimistic Christians choosing to believe this trope is the reason for the sudden onset of the End Times and God isn't really a vindictive, short-tempered jerk who decided to get the ball rolling on Armageddon for no better reason than because he was in a worse than usual mood that morning and It Seemed Like a Good Idea at the Time. Unfortunately, they're completely wrong.
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Since the entire point of The Maker in Dragon Age is "faith", we may never get a straight answer as to whether He truly exists or does anything at all. Nonetheless, whenever Thedas faces a Darkest Hour, unlikely coincidences such as the right people being in the wrong places at the wrong times give the world a fighting chance. This becomes especially important in Dragon Age: Inquisition, which has Faith as its Central Theme. In the wake of the latest disaster, the peoples' faith is tested, and many wonder whether The Maker has abandoned them or if He even existed in the first place. By the end of the game, those questions remain unanswered...after Thedas is saved once again by a string of coincidences. Solas believes that this is how gods should behave, since no true god needs to prove its power to anyone. Solas isn't certain whether The Maker exists, but he approves of the idea of The Maker. By contrast, he believes the Elven Pantheon and the Old Gods of the Imperium existed, but does not acknowledge them as true gods. This takes new meaning after The Stinger reveals that he is a member of the Elven Pantheon, Fen'harel the Dread Wolf.
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In The Colour of Magic, it turns out that the gods do in fact play dice with the universe — as in, many of the seemingly capricious plot events that befall the heroes turn out to be manifestations of a complicated game of Dungeons & Dragons between Fate and The Lady.
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Kids Praise:
In some albums, God directly intervenes or speaks to Psalty when Psalty is at a particularly low point, but in the ninth album, God provides a means of replacing the missing album that Risky Rat stole, which only happened because of the ninth album's adventure in the first place!
During the Time Travel plot of the seventh album, Psalty and the kids appear in a few places and times where having a bunch of singing kids and a supernatural One-Man Band like Psalty would actually be helpful! These include a tent meeting where the musicians never showed up, a music printer who just modified a song and wanted to see how it sounded, and meeting Psalty himself when he was a child.
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Spell My Name with an S: Two non-corporeal people, on a bet, manage to completely avert nuclear war just by convincing one man to spell his name with an S instead of a Z.
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In The Bible: The Complete Word of God (abridged), Solomon is asked to give his wisdom on how God in the New Testament could be so different from that in the Old Testament. His answer, in a word, is Bewitched:
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Falling Sideways has a plot consisting more or less entirely of the main character being jerked around, tricked, told lies, arrested, told more, contradictory lies, framed, abducted by aliens, told yet more lies and finally being given most of British Columbia, thanks to the plans of a godlike figure whose real motives are an absolute headache to work out and who seems to suffer from major Complexity Addiction. Discussed around the third or fourth set of elaborate falsehoods, with the protagonist cracking that all of the moving in mysterious ways is clearly God ducking to avoid the things being thrown at Him.
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The Alloy of Law: During the final battle, Wax runs out of weapons and metals, and snarkily prays to his god, Harmony, for help. He is very surprised when Harmony actually answers, explaining that there's not much he can do in situations like this, especially since he wants to preserve free will. Wax asks why he couldn't at least do something, and Harmony says "I have done something. I sent you." Then Wax sees his weapons chest, thought lost much earlier in the story, sitting not ten feet away from him.
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Tokyo Godfathers ties the fates of three homeless bums with that of an abandoned baby called Kiyoko. There are Contrived Coincidences, multiple girls with the same name, and multiple destinies converging on this one baby. Hilariously, it works.
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In Endstone, Kyri thinks she must have faith because of this. (Albeit "the gods" rather than one.)
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Spoofed in an episode of Taz-Mania where the Bush Rats start worshiping Taz's little brother's rubber ducky. When it's inevitably reclaimed by its owner, the Chief assures the other Bush Rats "The gods work in strange ways. This is just one of the stranger ones."
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Saturday Morning Breakfast Cereal:
Parodied here, in which the phrase is used to explain why a nun was sent to Hell.
Also used in a comic about theodicy here, with a minor add-on to the phrase.
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Judge Frollo makes such a remark in The Hunchback of Notre Dame (Disney), when mentioning that Quasimodo may end up being useful to him. There's arguably also a straight example carried through the film itself; had Frollo drowned Quasimodo as an infant, many future events would not have taken place; Phoebus would not have found the Court of Miracles on his own, for example. Quasimodo's presence, along with that of Esmeralda, is one of the biggest driving factors in Frollo's downfall.
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In The Divine Comedy's Heaven, the Eagle of Justice happily explains the inexplicable presence of two pagans in Heaven by revealing that both of the kings came to know Christ and reject paganism by circumstances lost to history. With this in mind, the Eagle praises God's predestination and implores mankind not to act as if they know who and how God will save.
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The Dresden Files:
This trope is invoked on several occasions, usually by Knights of the Cross. Harry usually does not take this as an acceptable answer.
Lampshaded in one of the later books, with Harry basically asking someone "They tried the 'mysterious ways' line on you too, huh?"
In the novel Small Favor and the short story "The Warrior", the archangel Uriel deconstructs Harry's criticisms of the "mysterious ways" explanation, illustrating how through apparently random, unconnected events God had used Harry to change many people's lives for the better without him even being aware of it. Uriel further points out that it only seems mysterious to Harry because God is omnipresent and omniscient, operating everywhere, at all times. What seems incomprehensible to a mortal's point of view, rooted in a single space and time, is not nearly so to God.
When Murphy contemplates how can the garden of the Carpenters be still green so late in the autumn, Harry answers: "Sod works in mysterious ways."
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Supernatural:
God's presence is zero for the first three seasons. Then, in season 4, He sends an angel to revive Dean from Hell and starts being a lot more proactive. When Dean questions Castiel about it, Castiel begins to state this trope, but Dean cuts him off and warns him, "If you say 'In Mysterious Ways,' so help me I will kick your ass." A later episode shows that God's ways are so mysterious that even Castiel doesn't know what's going on.
The archangels, and Lucifer, all seem very certain that their father is real, but that he is either dead or just gone forever. As one might imagine this distresses them. Castiel wants to find him and ask what's up.
They found out from an angel named Joshua that God is on Earth and aware of Apocalypse, but simply doesn't care. Cue to severe despair for Dean and tremendous loss of faith and start of severe alcoholic problems for Castiel in following episodes.
Later, it is implied that Chuck, the prophet who began writing Dean and Sam's adventures for profit, might have been God the whole time and was slightly guiding them. Of course, considering some hints from Gabriel, Lucifer and others and the way all angels and humans are, it still doesn't excuse him of being one hell of a lousy father, considering Gabriel decided to ditch them and turn into the Trickster, Lucifer... well, you know the rest. In retrospect, this means that when Chuck was apologizing for making them live bad writing, he was apologizing for their entire lives.
In the episode "Reading is Fundamental", Castiel outright invokes this trope by reacting to Dean's question on what kind of sense some angelic plan makes with "That's God and his shiny red apples."
In season 11, we finally see that Chuck was God all along when he intervenes to save the boys' lives from a mysterious plague being spread by the season's Arc Villain, The Darkness.
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Discworld:
In The Colour of Magic, it turns out that the gods do in fact play dice with the universe — as in, many of the seemingly capricious plot events that befall the heroes turn out to be manifestations of a complicated game of Dungeons & Dragons between Fate and The Lady.
There is no god involved, but in The Science of Discworld III: Darwin's Watch, Hex claims that the voyage of the Beagle was almost as significant an event as Joshua Goddelson leaving his house by the back door in 1734, leading to commercial nuclear fusion being perfected 283 years later.
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In Slumdog Millionaire, justification is given for the main character's crapsack life story, and eventual rise to the richest of the rich, in three words: "It is Written." For every question on Who Wants to Be a Millionaire, except for the last, Jamal knows the answer by virtue of some dramatic or important event in his life, to which we are treated.
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In Saving Grace, God's plans for protagonist Grace Hanadarko, the nature of angels or the reasons for giving her a shot at redemption, thus often investigated in many ways, will stay mysterious to her until the very last episode.
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Special Circumstances has several characters discuss this point. One character points out that no evidence for the existence of deities has ever been found in controlled circumstances. Another character rebuts this by pointing out that the researchers are working in the world controlled by an all-powerful being who actively does not want them to find evidence for the being's existence, and so will go out of its way to subvert the tests for its existence. Further, the character points out the anomaly of sub-atomic particles acting as both particles and waves, asking "What more proof do you need for the ineffable nature of the universe?"
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The four are baffled by many of the changes made to C'hou in The Keys Stand Alone: The Soft World since they left six years ago. The general explanation is that "the gods changed it", and they learn directly from the gods themselves that they made the changes to please both the G'heddi'onians and the skahs. This doesn't suffice; very little makes sense to the four, such as the obviously ancient cliff dwelling that seemed to have been created only three or four years ago. Why make it ancient? However, everything makes a lot more sense after they find out that they're in a giant telepathic MMORPG, the gods are fake, and the changes were made because of the Rule of Cool.
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Cat's Cradle introduces the religion of "Bokononism", wherein all living beings are arranged by God in groups called karass, in order to advance the divine will. The members of a karass may never even know each other, and their work may overlap in bizarre, coincidental ways, but they work together for a single purpose that they'll never know. Of course, Bokononism also admits that it's all bullshit.
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Tolkien's Legendarium:
It's implied throughout J. R. R. Tolkien's work that Eru (AKA God) has his hand in everything. Gandalf in The Lord of the Rings explicitly states that "Bilbo was meant to find the Ring in The Hobbit, and not by its maker." It's more complex than that, since one of the Gifts that Eru gave to Men (including hobbits; as opposed to Elves) was true free will in the sense of fighting fate. As is pointed out in Unfinished Tales of Númenor and Middle-earth, Bilbo was meant to find the Ring, and Frodo was meant to bear it, and Gandalf was meant to guide them both. But Bilbo and Frodo could have refused to leave home, and Gandalf wasn't "even allowed to try" to compel them. And Gollum slipping in the Mount of Doom to his death was stated by Tolkien to be His direct intervention.
As an Angel Unaware, Gandalf himself fell under this. Unlike conventional wizards he didn't go around throwing fireballs or magic missiles but instead acted in subtle ways, singlehandedly raising the morale of just about every good-aligned faction throughout the trilogy and encouraging every promising individual to live up to their full potential.
In The Fall of Gondolin, Tuor is following the stream which flows through the Rainbow's Cleft when he notices three great gulls flying overhead. Ulmo the Lord of Waters/the Ainur then put into heart the desire to climb the ravine's left wall to watch the unfamiliar birds more closely, thus saving him from death in the rising tide and ensuring that he finally escapes from Hitlum.
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Parodied in Fable III. After completing one sidequest, the villager you helped exclaims that the gods must have sent you to help him out. He then starts to examine this idea more deeply and reasons that it would be logically inconsistent to credit good things to divine will whilst at the same time writing off the bad as mere misfortune. Hence, not only was you saving him all part of the plan, but so was him getting into trouble in the first place, the stress he went through, and every minor problem he's ever faced. He ends up despairing at a Universe that is at best indifferent to human suffering and at worst actively malicious.
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Parodied on American Dad! when Stan meets God after learning his family is about to die.
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The World of Darkness:
Demon: The Descent: The angels of the God-Machine have missions, but they can look at the larger consequences (in fact, that's often how their descent into demon begins). Word of God casts them as more similar to the Observers on Fringe or the Strangers in Dark City, agents of the great machine who keep the machinery working.
One demonic faction, the Integrators, believe that even their fall from grace serves a larger purpose to the God-Machine, and that they need to eventually return to the G-M to fix something broken within it. This point of view is tough to sell to other demons.
The God-Machine will occasionally do things even demons find bizarre, like sending two angels to Earth with conflicting purposes (which practically guarantees that one or both will fall), or send Exiles, angels who arrive with a nonsensical, unachievable purpose or none whatsoever.
Promethean: The Created: The qashamallim are "angels" made of the same Divine Fire that gives Prometheans life, but lack free will. They manifest for only a short while, and have one particular purpose they must complete in that time. This purpose can range from bringing two people together to destroying a city, all in service of "the Principle".
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Quantum Leap: At one point, Al theorizes that "God, time, fate, whatever" is responsible for Sam's leaps, as something is obviously helping Sam leap into people who need help. In the series finale, Sam meets that "something" in the form of a bartender. The bartender points out that, contrary to what Sam believed, his leaping has had a significant impact on the world. Sam may have only helped one life at a time, but those lives touched others, and those others. The bartender congratulates Sam, telling him that he has done a lot of good. This convinces Sam to continue leaping instead of trying to get back home.
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The End of Eternity: The Eternals make minor adjustments to humanity's timeline to reduce the number of butterfly effects. At the very start of the novel, the protagonist changes the course of history by moving one particular item to a different shelf. These "mysterious ways" are a well-studied branch of mathematics, but even still they come with a number of unintentional side-effects.
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In The Legend of Zelda, the Golden Goddesses rarely intervene in mortal affairs and have inscrutable motivations and methods. Even the Greater-Scope Paragon Hylia, a lesser goddess herself, can only theorize the reasoning behind their actions. The Goddesses are the embodiment of goodness but allowed Ganondorf, the reincarnation of a God of Evil, to wield part of their power through the Triforce of Power (as well as the entire Triforce in The Legend of Zelda: A Link to the Past) supposedly since as a Gerudo he was still one of Din's children. They normally give the Hylians the tools to oppose him themselves, and the one time they did directly intervene they caused The Great Flood and wiped out most of the planet.
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Promethean: The Created: The qashamallim are "angels" made of the same Divine Fire that gives Prometheans life, but lack free will. They manifest for only a short while, and have one particular purpose they must complete in that time. This purpose can range from bringing two people together to destroying a city, all in service of "the Principle".
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Gimmicks Three: Shapur tells Welby that by signing the contract, he will be blessed with supernatural good fortune for ten years, causing every wish Welby makes to be fulfilled by seeming coincidence. Welby's good fortune would occur if he placed faith in either God or the contract. Demonic contracts cannot go against the Will of God.
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Immortal Hulk: Mentioned early on with the story of the Book of Job, in which Job asks God for an answer as to why his life was ruined and gets a response he cannot comprehend. In the last issue, Hulk and Joe Fixit come face to face with the One Above All, and Hulk asks why his life is so horrible. The One Above All responds in a similar fashion, soon irritating Joe, who figures he's not going to give them a straight answer. It's then implied that this was itself a plan.
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The Garden of Sinners: This is how the Nasuverse's Counter Force works. A series of events and choices, each of them meaningless on their own, were "nudges" to get Shiki in just the right place and time to stop Araya from destroying the world. This method can fail if the Counter Force's selected agents don't perform their tasks properly or the threat manages to overcome them. If the situation becomes unrecoverable, Counter Guardians arrive to eliminate the threat and everyone within a few miles or so.
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Each of the talking toys in Wonderfalls will repeat a short phrase to Jaye, who has to act on what little evidence she has for a generally beneficial result (or else they will harass the shit out of her). One episode has a toy penguin tell Jaye, "Bring him back to her!"; after some desperate flailing, Jaye manages to a) restore a nun's faith in God, and b) reunite a priest with his wife and daughter. In some episodes, Jaye deliberately decides not to follow the advice of the toy animals, which still results in everything working out right.
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In Hellspark, Tinling Alfvaen is a "serendipitist", which means she possesses a psychic power that causes things to turn out well when she's involved, sometimes in ways that don't seem so lucky at first. Nobody understands how it works, just that it does. Shortly before the novel starts, she's fired because her employer figures that nobody whose serendipity is working at full strength would catch an incurable disease like she just did; it turns out that she needed to have been fired in order to be in the right place at the right time later on. And before the book's over, the incurable disease has been cured, thanks to a chance meeting with a biochemist who finds her case interesting, on a planet she went to for other reasons without having the slightest idea it had any biochemists of that caliber.
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The Empirium Trilogy: Taliesin says that the Empirium "works in mysterious ways" as a way to dismiss Rielle's concerns that the prophesied Queens are going to appear soon.
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Pony POV Series: Defied by the Alicorn Elders. Being living embodiments of Wisdom and Empathy, they have no reason not to be straightforward in their rare interactions with mortals, and do not manipulate things in their favor, being strong believers in free will.
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The Elder Scrolls:
Anu, the God of Gods Anthropomorphic Personification of the primordial force of stasis/order/light. It is said that his presence is a force "so prevalent as to be not really there at all". It's theorized that this is in part because mortals have a much tougher time envisioning "perfect stasis" than they do "change".
The Aedra, who formed out of the spilled and intermingled blood of Anu and his "brother" Padomay, sacrificed much of their divine power when they were convinced/tricked into creating Mundus, the mortal plane. As such, they prefer a much lighter touch when influencing mortal affairs, leading to this trope. At most, they'll empower a mortal agent to handle their affairs, such as Akatosh sending the "Last Dragonborn" to oppose Alduin in Skyrim. In the rare event that they do pull a Divine Intervention and directly intervene at full power, it is to prevent the full-blown End of the World as We Know It, as Akatosh did at the end of Oblivion.
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Good Omens:
Near the beginning of the book, it is said that God does not play dice with the universe; rather, He plays an ineffable game of His own devising which might be described from the vantage of the other players, i.e. everybody, as 'playing a complex and unintuitive version of poker in a pitch black room with blank cards for infinite stakes, with a dealer who won't tell you the rules and who smiles all the time' (paraphrased).
Near the end of the book, Crowley points out to Aziraphale that an omniscient, omnipotent god would never have allowed them to prevent the apocalypse, or for that matter have allowed Lucifer's rebellion unless that was what He wanted all along. He goes on to suggest that the war between Heaven and Hell isn't so much a chess game as an incomprehensibly complex game of solitaire.
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In the Futurama episode "Godfellas", God/satellite/satellite-which-collided-with-God believes that God should behave in a mercurial fashion. Unlike many examples, it actually explains why it believes this way: if a deity does too much for its people, they will become dependent on it, but if it does too little, then its people will not be able to deal with problems beyond their abilities and will lose hope. By working in mysterious ways, the people are motivated to work hard and expand their knowledge, but can still receive help if they need it. This is a stark contrast to how Bender plays God to some tiny sapient beings living on him. By asking them to do him favors, he inadvertently introduces crime, while maiming and killing hundreds, if not thousands. By trying to help, he kills scores of them and destroys many of their crops. By doing nothing, those he hasn't paid attention to feel ignored and eventually wage all-out war that results in mutually assured destruction, using weapons built from Bender himself. Speaking with the nebula changes Bender, who goes out of his way to rescue trapped monks who Fry suggested God could take care of. Such an act is done of Bender's own will, but only because of the nebula's influence, so the nebula does save the monks, though they will not credit him, thus showing his philosophy in action.
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The Bible: In Romans 8:28: "And we know that in all things God works for the good of those who love him, who have been called according to his purpose." Which sounds hilariously idealistic, but it was written by an ex-criminal, so he knew what he was talking about.
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In the novel Small Favor and the short story "The Warrior", the archangel Uriel deconstructs Harry's criticisms of the "mysterious ways" explanation, illustrating how through apparently random, unconnected events God had used Harry to change many people's lives for the better without him even being aware of it. Uriel further points out that it only seems mysterious to Harry because God is omnipresent and omniscient, operating everywhere, at all times. What seems incomprehensible to a mortal's point of view, rooted in a single space and time, is not nearly so to God.
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Lucifer (2016): Amenadiel always tries to see his divine father's plan in the things that happen to him, and Lucifer always accuses "dear old dad" of meddling and trying to manipulate him, but it's never clear whether they're right or if they are reading design into what is just blind cause and effect. Late in the series, when God is departing for another dimension, never to return, Lucifer demands to know how much of what has gone before was part of His plan. God just smiles enigmatically and turns away.
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Joan of Arcadia: God will tell Joan to do something, for reasons that aren't immediately apparent, but which often make sense by the end of the episode. For example, in the pilot, God tells Joan to take a job at a bookstore. After coming home from work one night, Joan runs into a man who she thinks is God in another avatar, but who's actually the serial killer her dad's been following. Joan figures this out and escapes from his car, causing him to crash, which causes the police to find him and arrest him. It also motivated Joan's brother to get out of the house and get a job.
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In The Soldier Son, the Speck magic, as well as Orandula the god of balances manipulate the protagonist through a series of convoluted chains of events, most of them set off by tiny, seemingly insignificant actions, like giving a stone to Caulder Stiet, which leads to the discovery of gold in the plains, which leads to almost all Gernian troops being pulled from the Specks' land, thus protecting the Ancestor Trees from being cut.
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Leverage: While no proof of a divine plan is given in the aptly named episode "The Miracle Job", a priest named Father Paul is trying hard to save his church from being sold, but the corrupt business man has some thugs go and beat Paul before he can reach the City Council to ask them once again to not go through with the sale. This attack draws the attention of Paul's old friend, and protagonist, Nathan Ford and his band of thieves. After a series of gambits to take down the corrupt businessman, including faking a miracle by having a fake statue of St. Nicholas appear to be crying and then undoing the miracle by framing the businessman for it as though it were a PR stunt, the church is saved. At the end, Nate and Paul discuss things and Paul is thankful for the miracle. When Nate points out they did fake it, Paul quickly retorts, "Five thieves saved my church" and considers that the miracle. He may not have seen the whole picture in the middle when it looked like he might be defrocked for the fake miracle, but in hindsight, Paul believes that God was always trying to help him save the church, even if he didn't understand it then and there.
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Warhammer: Tzeentch, Chaos god of change, chessmasters, mutation, Chronic Backstabbing Disorder, magic and embodiment of all hope, exists purely to make stupidly-complex Xanatos Gambits that span millennia, and everything that makes one of those plots fail merely ensures that it causes another to succeed. In theory, everything that he does is part of some intricate, convoluted scheme intended to achieve some goal. In practice, nobody — not even his greatest daemonic servants — has the faintest idea what any given move might have been intended to achieve, whether something is or isn't a deliberate move by him, or even what his goals even are.
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In Signs, one child's asthma, another child's obsession with leaving half-full glasses of water everywhere, a washed-up brother's old baseball career, and even his wife's dying words were apparently all part of God's plan to restore a priest's faith by helping him foil an alien invasion.
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In El Goonish Shive, Voltaire references the trope when reassuring a private detective that the shady business he is getting involved in is for the greater good. The detective, however, has his doubts after seeing the blatant murder attempt on Elliot.
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In To Say Nothing of the Dog, no divinity is ever mentioned, but this is the way the universe corrects potential errors due to time travel.
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One of the most common interpretations of Princess Celestia from My Little Pony: Friendship Is Magic; despite doing seemingly very little, she seems to always have things set-up to turn out alright — even if such plans had to be so convoluted and unlikely to barely be noticeable at all. For example, is the only reason she was so calm about Nightmare Moon's return because she's somehow known (or arranged for) all the potential Elements of Harmony to be in Ponyville at the correct time? In "Celestial Advice", this is revealed to indeed be the case.
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In Alchemical Solutions, Autochthon. Sadly, not always in good ways.
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In All Clear, a theory is presented that the universe regarded the Germans winning World War II as such an error, and has since corrected it via time travel through amazingly subtle coincidences without anyone realizing it.
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In Nomine: Nobody — not the angels, not anybody else — truly understands God's plans and ways. There are certainly reasons to think that God continues to interact with the world, but His ultimate aims and His methods to achieve them are poorly-understood mystery that the angels can do little more that fret over. Mechanically, if you roll a 111 or 666 on a 3d6 roll, either God (on a 111) or Satan (on a 666) intervenes. What this means depends on which side of the War you're on, but the GM is encouraged to work in this method (for example, a demon doing something explicitly supernatural, on a 111, might discover a warrior angel — for reasons of his own — walking around the corner right as the Disturbance is traceable to him).
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Battlestar Galactica (2003) attempts to wrap up its sprawling tangle of unresolved plot threads at one fell swoop by invoking this at the end. The fandom was not amused.
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There is no god involved, but in The Science of Discworld III: Darwin's Watch, Hex claims that the voyage of the Beagle was almost as significant an event as Joshua Goddelson leaving his house by the back door in 1734, leading to commercial nuclear fusion being perfected 283 years later.
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In The Fall of Gondolin, Tuor is following the stream which flows through the Rainbow's Cleft when he notices three great gulls flying overhead. Ulmo the Lord of Waters/the Ainur then put into heart the desire to climb the ravine's left wall to watch the unfamiliar birds more closely, thus saving him from death in the rising tide and ensuring that he finally escapes from Hitlum.
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The titular agency in The Adjustment Bureau may or may not work for God, but their main approach is to gently nudge things in the "right" direction in order to follow "the plan".
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HZD Terraforming Base-001 Text Communications Network: Discussed in the conversation about miracles between GAIA (a Deus Est Machina who got resurrected after her Heroic Sacrifice due to an incredibly unlikely chain of coincidences) and Varl (a tribal human who belongs to a religion that might technically worship GAIA; he's not sure). As GAIA explains, it's impossible to prove the existence of the supernatural, because if you prove it, it's just more science. Therefore, she defines a miracle as "an extremely unlikely, advantageous coincidence, one that statistically should not have happened, or at least not in quite such a fashion." She comes off as surprisingly spiritual, believing that something above even her is looking out for the world.
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Ciaphas Cain: Cain considers the God-Emperor to be this, remarking several times that his life could have turned out radically different, but the Emperor works in mysterious ways and/or has a twisted sense of humor.
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Demon: The Descent: The angels of the God-Machine have missions, but they can look at the larger consequences (in fact, that's often how their descent into demon begins). Word of God casts them as more similar to the Observers on Fringe or the Strangers in Dark City, agents of the great machine who keep the machinery working.
One demonic faction, the Integrators, believe that even their fall from grace serves a larger purpose to the God-Machine, and that they need to eventually return to the G-M to fix something broken within it. This point of view is tough to sell to other demons.
The God-Machine will occasionally do things even demons find bizarre, like sending two angels to Earth with conflicting purposes (which practically guarantees that one or both will fall), or send Exiles, angels who arrive with a nonsensical, unachievable purpose or none whatsoever.
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Discussed quite a bit in Dice Funk's third season regarding the D&D pantheon. It's shown that gods can interfere more directly but that if they did the other gods would take it as an opening to enact their own plans and that this would ultimately be a really bad thing for everyone involved. Interestingly the one time when things are dire enough that several gods worked together to stop the World of Forms from turning, their characteristic caginess backfires because they never told anyone about the danger, causing an uninformed evil god to ruin their plans, ultimately killing every god as a result.
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In Constellations, Amaterasu convinces Taylor to start working at a rundown shrine, which in turn results in her doing chores for her neighbors for small favors. As a result, the local Japanese population is reinvigorated, Oni Lee becomes more human, and Sophia's arrest goes sour, turning Taylor's life around.
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Lords of the Underworld: The ending of The Darkest Passion implies that everything Olivia did in that book — including quitting her job in Heaven, becoming mortal, and getting attached to a Ragtag Bunch of Misfits that all the higher angels told her to stay away from — was predestined so that God could make her said misfits' Guardian Angel. The job of a guardian is so dangerous that He couldn't have ethically ordered her to do it before, especially for strangers she didn't personally care about at the time... but if she decides to protect them on her own and then He restores her angelic abilities, then that's different. This situation also explains how the Christian God can coexist with Greek gods in the setting.
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Bridge of Birds manifests this eventually, in a seemingly random, seemingly impossible way.
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The Second Try: When Shinji complains that he and Asuka have failed to change the past, Kaworu cites this trope and points out that even the small changes they've made have improved the outcome, resulting in Toji playing a critical role in fighting back the MP-EVAs. It also seems likely that Kaworu guided Rei and Aki into meeting, which was the catalyst for Rei refusing her role in Third Impact.
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In Lessons from the Mountain, during his soul's trial, Maedhros asks Manwë — the King of the Valar — why he never granted him a quick death when he begged for it during Morgoth's torture. Manwë replies that he intended to release him from his torment as soon as possible.
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The following is a list of statements referring to the current page from other pages.

 In Mysterious Ways
processingCategory2
Religion Tropes
 Tokyo Godfathers / int_f4edd0ac
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In Mysterious Ways
 Beast Wars: Uprising (Comic Book) / int_f4edd0ac
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In Mysterious Ways
 Clive Barker's Next Testament (Comic Book) / int_f4edd0ac
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In Mysterious Ways
 Halo: Escalation (Comic Book) / int_f4edd0ac
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In Mysterious Ways
 The Second Try / Fan Fic / int_f4edd0ac
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In Mysterious Ways
 Beyond the Outer Gates Lies... A high school library? (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 Children of the Force (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 Lessons from the Mountain (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 Ripples in the Pond (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 Scar Tissue (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 Steal Your Way In (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 Ultimate Sleepwalker (Fanfic) / int_f4edd0ac
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In Mysterious Ways
 A Serious Man / int_f4edd0ac
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In Mysterious Ways
 End of Days / int_f4edd0ac
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In Mysterious Ways
 Evan Almighty / int_f4edd0ac
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In Mysterious Ways
 It's a Very Merry Muppet Christmas Movie / int_f4edd0ac
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In Mysterious Ways
 Jackie / int_f4edd0ac
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In Mysterious Ways
 Michael / int_f4edd0ac
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 Miracle on 34th Street / int_f4edd0ac
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 The Adjustment Bureau / int_f4edd0ac
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In Mysterious Ways
 The Good Witch / int_f4edd0ac
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In Mysterious Ways
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In Mysterious Ways
 Mushoku Tensei / int_f4edd0ac
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In Mysterious Ways
 Mushoku Tensei: Jobless Reincarnation / int_f4edd0ac
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In Mysterious Ways
 Book of Job / int_f4edd0ac
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In Mysterious Ways
 Chicken Soup for the Soul / int_f4edd0ac
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In Mysterious Ways
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In Mysterious Ways
 Mushoku Tensei: Jobless Reincarnation / int_f4edd0ac
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In Mysterious Ways
 Proven Guilty / int_f4edd0ac
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In Mysterious Ways
 Small Favor / int_f4edd0ac
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In Mysterious Ways
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In Mysterious Ways
 The Colour of Magic / int_f4edd0ac
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
 Blackheart
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways
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In Mysterious Ways