The Monster Rats from From the New World, oh so much. Who serve as the main antagonists, especially Squeala/Yakomaru during the 3rd act of the series, as well as murdering Mamoru and Maria and kidnapping their child and raising it to serve them. Subverted in that aren't really any worse than their PK-using human overlords, and are in fact transformed humans.
In 1930s Mickey Mouse comics, Minnie's cousin Ruffhouse Rat isn't evil—but he's a lazy, egotistical flop of an athlete who essentially makes Mickey and Minnie solve his problems for him.
The Rat King from the cartoons is a subversion, as the rats were harmless until they were in the Rat King's power (and the Rat King himself was human).
In Blacksad the bar patron who helps Blacksad track down Leon Kronski and tries to kill him, turning out to be working for Statoc is a rat. Lampshaded by Blacksad in his internal monologue.
Averted in The Tale Of One Bad Rat, a miniseries about a teenager who runs away from home after being sexually abused by her father; her only companion is her pet rat, and she can get quite indignant when people say that rats are dirty or creepy.
As far as Disney films go, Lady and the Tramp features a rat that threatens the Darlings' baby but is stopped by The Tramp, and Cinderella features heroic mice who help the title character deal with her stepmother and stepsisters.
Averted in Oliver & Company though. The rats that show up during the "Why Should You Worry" scene may look rough on the edges, but they are not evil.
Averted in Ratatouille, where the main character is an intelligent, urbane rat with a gourmand's taste in food and the ability to cook like a classically trained chef. Of course, most of the other rats are classless, tactless layabouts, but at least they aren't evil.
In the Spin-Offshort, "Your Friend the Rat", Remy and Emile try to argue for the reconciliation of humans and rats, using historical facts presented to various styles of animation. Among other things, they explain that The Plague was actually caused by fleas that got attached to black rats, not by the rats themselves, and in fact, the brown rat had supposedly helped to end the Plague.
And then played with/double subverted during the end credits, when a cautionary message allegedly from the clip's producers scrolls by to remind the audience that rats are vicious, unsanitary, pestilent vermin, as Remy and Emile can be heard vigorously protesting in the background.
Also subverted in Ratatoing, a cheap knock-off of Ratatouille. Rats are both heroes and villains, being a Mockbuster.
The same goes in The Secret of NIMH. Except for Magnificent Bastard Jenner and Brutus (who, to be fair, is only doing his job), all the rats are benevolent. In particular, Justin is a hero who is designed to be as dashingly handsome as one can make a rat and still be recognizable as such. It should be noted that had Brutus wanted, he could have very easily killed Mrs. Brisby with that spear. Instead, he repeatedly intimidated her by swinging it in her direction, and didn't pursue her when she ran off.
Again again in Flushed Away, where the rats are, as a group, no more good or evil than any other random population.
Yet another aversion occurs in The Wind in the Willows with Ratty. Sure he's actually a Water Vole, but voles are close enough to rats for government work.
In Enchanted, the rats do a considerable share of the housework while under the influence of Giselle's "Happy Working Song". Only one mouse is seen to help out, and it's only there because a rat wouldn't fit in the bathtub drainhole.
In one adaptation of The Country Mouse and City Mouse, the bad guy was a rat.
The Mice in An American Tail are all virtuous, loving immigrants. Warren T. Rat, on the other hand, isn't even a rat, but a cat, and one of the bad ones at that. It also briefly features a huge, scary rat who is a sweatshop owner.
Chicken Run features rats who peddles junk to the hens in exchange for eggs. They're enterprising, but not evil.
In Coraline, she's shocked that the cat would kill a mouse like that. Little did she know...
This takes inspiration from Rowling's sister's phobia. Rowling herself doesn't mind rats. There is also a chapter that has magical rats showing off in a store, playing jump rope with their tails, so not every rat is portrayed as villainous.
In The Tale of Despereaux, the mice are all good (cowardly, but good), while the rats are all evil. Chiaroscuro the Rat, an innocent born into a corrupt society, has to deal with his species' stereotype.
Though they seem to get along with humans during the opening and ending.
The rats in Redwall are always criminals. They're even referred to as vermin.
By Loamhedge they seem to have taken back the word "vermin" for their own, as they actually refer to themselves as vermin and seem proud of it.
Played straight in The Book of the Dun Cow with Ebenezer Rat, an egg-eating and violent rat, although it should be noted that he is nowhere near the most evil character in the book and dies in battle with one of the real villains.
Played with in Garry Kilworth's Welkin Weasels series. The black rats are Always Chaotic Evil, while the Norway rats are lovable fops.
This sounds fairly close to their behavior in Real Life. Black rats tend to be solitary and agressive, and aren't even that common.
Similarly in his novel House Of Tribes: the rat, Kellogg, is evil and a murderer.
David the rat nothlit in Animorphs, although he was forced into rat morph to keep him from threatening the rest of the group. He does return just as evil in a later book, though.
Watership Down uses this one. The rabbits are attacked by a pack of rats just after escaping from Strawberry's original warren. Then again, later in the book Hazel, during the first trip to Nuthanger Farm, stops to ask a rat for directions and gets a quite civil answer, even if, as the narrative notes, the rat had no particular reason to be friendly.
Possibly the hostile ones were defending their home, as the rabbits had bedded down in an abandoned barn suitable for rats to live in. The rat at Nuthanger farm was simply walking by.
The correct answer being: all of them except the telepathic rats.
Much earlier, Pratchett subverted the "cute friendly mouse" side of this trope with Definitely Not Squeak, a mouse who began talking under the influence of Moving Pictures. He was outraged when told that mice are considered cute and sweet by humans, as he'd been the toughest mouse Badass in the house and proud of it.
In Reaper Man, Death acquires a sidekick, the Death of Rats, whose form sort of implies rats are similar to humans, as they conceptualize Death by anthropomorphizing it, rather than by picturing something that causes their deaths (i.e. the mayflies see Death as a trout.) Perhaps not Rats Are Good, but definitely Rats Are Smart, or Rats Are Like Us.
"Anything so much like a human has to have a soul."
Mostly averted in Mrs. Frisby and the Rats of NIMH, and its sequels and adaptations. Indeed, its author received a number of letters asking just why he had rats as sympathetic heroes in his book.
Zigzagged in The Roly-Poly Pudding, where it's unclear whether the rats actually intend to harm Tom Kitten or are just trying to scare him. (Conversely, there's no question that the cats have eaten rats in the past, and continue to eat them in the future.) This relatively even-handed treatment probably occurs because Beatrix Potter kept a pet rat when she was a girl.
The mouse part is subverted in The Hitchhiker's Guide to the Galaxy. Mice are actually the smartest animals on the planet Earth, which itself was a sort of massive, living distributed computing experiment to determine the Ultimate Question. When Earth is destroyed, they decide that they need to get what data they can salvage by cutting it right out of Arthur Dent's brain.
Avram Davidson's short story "The Tail-Tied Kings" deals with a rat warren threatened with destruction by their "slaves" (the humans they steal food from) and the escape of the aforementioned Kings (and Queens).
Bubo, a rat hero of A Night in the Lonesome October is introduced as a familiar with a knack for shady deals and corresponding manners. He turns out to be much more sneaky, but in general a pretty decent critter.
Rats are quite some pests on Warrior Cats, but the most evil is seen on Firestar's Quest, where a rat speaks cat language and hints that his kind drove out the former SkyClan. And then, there were the rats that caused almost all of ShadowClan to get sick in Rising Storm...
Subverted with Mr. Ratburn, the teacher from Arthur. Although he has a reputation as a Sadist Teacher (mostly because he gives a lot of homework), he is actually very kind and helpful, and he puts on children's puppet shows in his spare time.
Of course, he's a water rat, which are technically voles and therefore less disreputable than true rats.
Averted with Jade Rat in Half World, who is a faithful friend and ally of the heroine, even if she is a bit of a Deadpan Snarker.
A new breed of large killer rats are the villains in a series of novels by the English horror author James Herbert.
In the Garrett, P.I. novels, the intelligent race of ratpeople are targets for a massive degree of Fantastic Racism, and even Garrett himself tends to regard them as thieving, craven, subhuman scum early in the series. He gets over it once Singe comes into his life, but she herself admits that far too many of her people won't even attempt to rise above their nasty reputation.
One episode of the Red Green Show has a song about this:
(Brackets indicate Harold singing) ♪ He comes down the chimney on Christmas Eve ♪ After we've all gone to bed ♪ He's not all that nice or jolly ♪ Until after he's been fed ♪ He's got beady eyes, and yellow teeth ♪ And his fur drops off when he moults ♪ His tail kinda wiggles and dances and jiggles ♪ Like a snake takin' 300 volts! ♪ He's Cheesy! (Cheesy!) The Christmas Rat ♪ Long and smelly and pretty darn fat ♪ Cheesy! (Cheesy!) The Christmas Rat ♪ Dropping a little surprise in your hat ♪ He comes with a gift! You don't have to beg! ♪ He's here to give everyone bubonic plague! ♪ Cheesy! (Cheesy!) The Christmas Rat ♪ And that's why everybody..... should have a gun! ♪ Merry Christmas.
Played with in Yes, Minister, when protesters keep Sir Humphrey from clearing a particular copse of trees because it was home to a family of badgers. He convinces them that there are no badgers in the woods, only rats, and the protesters leave.
Averted with Rizzo the Rat of The Muppets, and his rat friends, who are genuinely friendly (except when you say the wrong things). Although they are still greedy and gluttonous.
Nature shows about snakes and similar predators tend to show them killing or swallowing rats, even if they aren't a major part of the predator's natural diet. This is because rats don't garner much sympathy from viewers: if a snake eats a bird, frog, or rabbit, it seems like more of a Downer Ending than if a rat becomes lunch.
In Fawlty Towers where Manuel's pet 'Siberian Hamster' becomes a pest that must be got rid of before the health inspector arrives. Note that there is nothing in this episode to actually suggest the rat is anything other than a good pet (and Sybil even refuses to release the domesticated rat into the wild on the grounds that it wouldn't be able to defend itself), the problem is simply that after a litany of public health offences that need to be resolved before the inspector returns, having a rat loose in the hotel is obviously a major problem.
For some reason Frasier and Niles Crane are both squicked badly by Daphne's description of the show rats she used to raise. All they can think of is the rats of the Black Plague, despite the fact they are both mental health professionals who should be familiar with the use of rats in psychological and medical studies. In another episode it's revealed they themselves were named for their mother's lab rats.
Previously, on Cheers, Frasier had a bizarre reaction when his psychologist wife made a pet of her experimental rat and, upon its death, tried to carry it to the park to bury it. He may have a phobia.
The mythology surrounding the phenomenon of the rat king (a group of rats whose tails are knotted and matted together with filth) tends to give them certain supernatural and generally unpleasant powers. Though it did (rarely) happen in real life, increased hygiene means that rat kings are probably not likely to occur ever again.
Also, Rat Kings refuse to manifest under controlled conditions.
The Rat is considered to be the first of the twelve animals of the Chinese Zodiac, and stories of how it achieved that status usually depict the Rat as having tricked the Ox and/or the Cat so it could claim that place for itself.
Averted in Hinduism, in which rats are held to be sacred by the faithful of Karni Mata. Her devotees are said to be reincarnated among the rats that live free and are cared for in her temple.
Averted in one Garfield strip where he meets three rat siblings, Rip, Bob, and Juanita, who are friendly.
"Three Skeleton Key", a 1950 episode of Escape narrated by Vincent Price, involves a trio of lighthouse keepers who find themselves besieged after a derelict ship crashes onto the nearby rocks and ejects its "passengers": an army of ravenously hungry rats.
Most rodent creatures in Magic: The Gathering are Green (the color of life) except for rats. All rats are Black (the color of death).
However, Dark Is Not Evil, and while many rats are in fact pests, some of the Kamigawa block Nezumi are decent, if anti-heroic.
And then there's Planescape's Cranium Rats — one isn't smarter than a normal rodent, but their telepatic abilities bind their little powers and intellects into Hive Mind, so the pack of three dozens can cast minor spells, half-hundred is as smart as an average human, and so on. They're Neutral Evil, and some or all of them are spies of illithid god Ilsensine.
Averted with normal rats. They're true neutral and can become familiars, just like other small animals.
Likewise, Pathfinder averts it with the Ratfolk, who are humanoid rats, but generally decent, friendly people, most commonly seen as wandering traders and tinkers who ride perfectly tame giant rats.
Subverted by the Nezumi (aka "ratlings") in Legend of the Five Rings; they're primitive and rather crude, but basically good guys.
When Five Rings was converted to Dungeons & Dragons for the 3rd Edition Oriental Adventures book, nezumi were portrayed as Chaotic Neutral. However, the book noted that ratlings were often evil in other settings.
The Ferrans of Talislanta tend to be nasty, thieving little scavengers. They have no concept of hygiene and can spray like skunks. However, the Ferran in the Talislanta tie-in anthology manages to be something of a Woobie.
The Beshilu of Werewolf: The Forsaken are Hosts, spirit parasites that possess humans, hollow them out body and soul, and ride around the resulting meat puppet. They're singularly obsessed with gnawing open holes in the Gauntlet, leaving gaps to the Shadow that allow pretty much anything to slip through unfettered. The werewolves don't like this; they wouldn't mind being able to get to and from the Shadow more easily, but the Beshilu are so filthy that they practically breed spirits of disease and madness, which then jump right through the Gauntlet holes, meaning anywhere they go is a hotbed for plagues and destruction.
The predecessor game, Werewolf: The Apocalypse, had the Ratkin, one of the many Changing Breeds. They decided the werewolves weren't going far enough in their quest to save Gaia from the deprivations of the Wyrm, so they basically became chaos-mongering terrorists and saboteurs.
The Mouse King in the Nutcracker Ballet is probably one of the more famous examples and a subversion of the "mice are nice" part. He even has three heads in some versions of the story.
See "rat king" under mythology. Now, imagine that in place of one guy in a costume with three heads. No wonder all the other characters are terrified of him.
The Burmecians of Final Fantasy IX are anthropomorphic rodents. The word 'Rat' appears to be a derogatory term for them, but they are mostly on the side of good.
Apparently most of the Rattkin in Wizardry are thieves (there's also a Rattkin scientist), and their high-ups are The Mafia, but in general they are not worse than any other faction present and better than some, and no more or less prone to generate an aggressive Random Encounter. That's just their ways. In Wizardry 8 some work with the party against Big Bad — it turns out that NPC followed him to another planet to avenge for crossing them on Guardia back in VII.
Rattata and Raticate in the 1st generation of Pokémon. They aren't really evil, but are often used by Team Rocket grunts and are Com Mons, so most players generally get tired of seeing them. Also, are contrasted by the Nice Mice Pikachu and Raichu.
Don't forget the army of anthropomorphic rats in Battletoads. These sleazy space pirates fit this trope perfectly. And you'll come to hate rats after Scuzz.
Jimmy Two-Teeth in the Sam & Max games, a small-time ruffian rat and Butt Monkey. He is apparently sent on a bus in Season 3 — but not before (it is suggested) causing an outbreak of bubonic plague at Max's bidding.
In Majesty Ratmen are a milder version of Warhammer's Skaven; they're like goblins, except their habitats are broken sewer pipes, which means they can pop up randomly in the middle of your town rather than some distance away.
Rats are almost always evil disease-carrying pests in The Elder Scrolls series. One notable exception is the initial Fighter's Guild quest in The Elder Scrolls IV: Oblivion. You have to save a woman's beloved pet rats from hungry mountain lions. In Skyrim they are replaced by Skeevers, which are even bigger, uglier, and filthier. One of the Thieves' Guild quests pits you against a wizard who went crazy trying to convince people that Skeevers are awesome. He now plots to overrun Whiterun with a swarm of mutated venomous Skeevers. Interestingly, it seems that Skeevers aren't always bad either. The owner of the Winking Skeever inn in Solitude named the inn in memory of his beloved childhood pet Skeever.
Slade the thief in Shining Force II causes the entire mess which you spend the rest of the game fixing, but to his credit, he eventually assists in correcting his mistake, and he even turns out to be one of your most valuable allies.
In Tales of Symphonia you encounter these in the sewer level of the game. At first they're not much of a challenge because by now your party is overleveled, but the plot requires you to shrink down, and suddenly a 12 foot rat is a lot more intimidating...
Inverted in Digger, in which sacred rats assist the keepers of the temple library and protect the books from gnawing insects. "Mousie", conversely, is what Ed called Digger, who is tough as nails and far from cuddly or helpless.
The Animals of Farthing Wood have a whole swarm of rather cartoonishly evil rats, considering the otherwise more realistic tone of the show. The rat king, Bully, displays all the stereotypical traits you'd expect a fictional rat to have: he's sneaky, boastful, ruthless, filthy, and cowardly, and his followers aren't much better.
This trope is averted in real life. Rats are actually friendlier, more easily trained, and less likely to bite than mice are, and thus make much better pets than mice do. Anyone who has worked in a pet shop can attest to this. While a mouse that is regularly handled can become quite friendly, other mice tend to be jittery and sometimes aggressive. Rats, on the other hand, are friendly and inquisitive right off, and quickly learn that a human arriving means it's time for food or play. Experiments have shown that rats are one of the few animals besides humans and higher primates proven to have a sense of compassion.
One rat-care expert has observed that fancy rats are the most human-like of all domesticated animals: omnivorous, adaptable, intensely social, living in large communities with multiple breeders, and capable of manipulating objects with their front paws.
A remarkable number of creators who avert this trope in their works had pet rats as children.
Some laboratories that use rats have reported students who felt extremely uncomfortable working with the rats because they started to become bonded to them.
Inverted by the HeroRATS: Giant Gambian pouched rats which are trained to sniff out land mines in their native Africa, thus allowing thousands of refugees in war-ravaged regions to safely reclaim their farms.
Rats killing mice is Truth in Television, usually for food. They will not kill mice (at least not on purpose) if they are raised and are familiar with them, however.
Nazi propaganda infamously equated Jews with rat infestation.
American propaganda during World War II also frequently did the same with the Japanese.
Henry Rollins once worked in a laboratory that experimented with mice, rats, and rabbits, as he tells in one of his spoke-word routines. One rat was extremely aggressive and refused to die, even after Rollins tried to kill it. This trope is subverted, in that Rollins took that as a lesson in strength.