Need to show how the Phlebotinum Du Jour affects living things, but the character isn't evil enough to test it on an animal? Well, plants are fair game. Therefore, plants tend to get mistreated a lot in fiction.
Are you a scientist who wants to test your new mystery formula? Just take an eyedropper and drop a few drops in the soil of your Philodendron. If it's a miracle cure, the plant will go from wilting to flourishing — and possibly to horribly mutated. If it's deadly poison, as it so often is, it will go from healthy and green to a sad pile of ashen leaves and shriveled vines. (Do note: for added drama, the plant will often wait to transform until you're sure that nothing is going to happen and leave the lab disappointed. Then it will probably turn into a monster and start wreaking havoc.)
Do you suspect that your friend is infected with The Virus or some sort of radioactivity? Do you want to make sure it's still safe to go near him? Have him go near a potted Ficus. If your friend is dangerous, the tree will instantly shrivel and die, all its leaves falling off at once.
Is your friend a Lethal Chef, but you don't want to hurt their feelings? Do you just want to make sure their cooking is safe to eat? When they're not looking, dump the -er- food into the Dracaena's pot. The plant will probably curl its leaves and die at once from the toxic substance meant to be comestible. Good thing you didn't eat it. It works with drinks, too.
Incidentally, none of these tests would work so well in real life. If you're paying attention at all, you may have noticed that humans and plants are very different living things. It should be noted that most of the plants you see out your window today are the ones that are the most resistant to disease and dangerous substances. Houseplants are often specifically marketed as air purifiers, meaning that they are also very resilient to the kinds of things that would easily make an animal sick. And we haven't even touched how long it could take for the substance in question to be absorbed into the soil, and then absorbed from the soil into the plant, and then for the substance to actually start killing the plant.
Vegetation is also apparently an excellent barometer for magical evilness. Has your character gained incredible nature-based powers and is Friend to All Living Things? Flowers and plants will sprout wherever she walks. Meanwhile, the Enemy to All Living Things is likely to be surrounded by dead trees and blackened grass.
Despite what the name implies, has nothing to do with either That Poor Cat or That Poor Car. Also please refrain from adding examples where plants are harmed by situations other than those described above.
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Anime and Manga
In the Fullmetal Alchemist two-part episode, "The Other Brothers Elric", Fletcher and Russell save Xenotime from the impending flood of red water by having all the trees in the surrounding area soak it up like a giant tree drain. All the trees are (apparently) then destroyed by the brothers.
In One Piece, just following the Little Garden arc, we get a small preview of Crocodile's powers when he expresses his annoyance with Mr. 3 by using a Touch of Death to make a rose wither into dust.
In one episode of Slayers, Xellos made a vegetable stew so noxious, the ingredients were screaming in pain... Taking part of a cooking competition though, he thought the whole idea was to kill the competition.
In the The Adventures of Tintin story Flight 714, when Captain Haddock is given a glass of health tonic by an eccentric millionaire, he dumps it onto a Ficus. The plant immediately starts dropping its leaves.
Papa Smurf once had an experiment with a daisy gone awry.
In Hawkeye Annual #1, Madame Masque attempts to drug kate. Kate takes a fake sip of the wine and then dumps it in a pot plant. The result is this trope.
In I Won't Say L relates that he once managed to kill a cactus by forgetting to water it.
Film - Animated
Used hilariously in the film The Emperor's New Groove - a cactus ends up turning into a topiary llama after Yzma pours some (what she thought was) potion-induced drink into it, only to find out after it transforms Kuzco that it was actually "extract of llama". Earlier, she got the idea to poison Kuzco when she, in full Evil Plan gloat-mode, accidentally knocks a vial of poison onto a plant, providing us with the current page image.
In Shrek 2 - Shrek sneezes the potion that'll make him look attractive onto a mushroom, and as the group walks away it turns into a pretty rose.
Scary Movie 2 has Shorty using a Psycho Serum on his marijuana plants. The plant later grows, becomes sentient, and starts smoking Shorty like he was a blunt.
Abbott and Costello's movie The Naughty Nineties had a hilarious scene where the Big Bad and Costello's character Sebastian are put alone together in a private room in a theater, where she proceeds to poison his drink. They then do a Poisoned Chalice Switcheroo back and forth until he gets confused and opts to toss the drink in the fern next to him. Sebastian watches the fern die very slowly, and then wipes his glass very thoroughly on his tux.
Ur-Example: In Hawthorne's "Rappacini's Daughter", the title character is so poisonous that ordinary plants wilt when she touches them.
Crowley and his plants in Good Omens. They're the healthiest houseplants in London, and the most terrified.
Aversion: In The Belgariad, Garion's recently-discovered cousin Adara asks for him to show his magic powers by making a bush bloom again. Garion refuses since it's winter and the bush would die. He then creates a new flower for her out of a twig and grass.
The flower is decidedly lopsided, puny, and... well, it's lopsided, let's leave it at that. Give Garion a break; it's his first go at live transmutation. It's nicknamed Adara's Rose, because Garion really, really loves his beautiful Algarian cousin, (or so Ce'Nedra thinks), and it does have a nice smell. And oh, did we mention it's a sovereign specific, cures any poisoning? Imagine wearing anti-poison as a perfume (Sadi wonders if it works as antivenin as well; we never do get to find out). One of the funnier scenes in the Malloreon plays out during this arc, especially when Belgarath tries to get the plant to grow.
In Thief of Time, one of the History Monks teaches novices to be wisely-cautious about the procrastinators by setting an apple on a table and accelerating time around it. Within seconds, it's rotted away and left behind a circle of frail, stunted tree seedlings that sprout from the resulting lump of mold.
Averted in Busman's Honeymoon. When Lord Peter Wimsey is offered some homemade parsnip wine, his wife Harriet, realizing the distress of a world-class oenophile, suggests he dump it in a nearby potted plant. However, Lord Peter goes ahead and drinks it (not without a shudder) after observing that the plant already appears unwell.
Live Action TV
The old 1950s The Adventures of Superman series had the Radioactivity example. Superman gets exposed to Radiation and goes into self-imposed exile. He's lonely and wants to be around others, so he put his hand out over a potted plant. But he's so radioactive and deadly, the plant dies on the spot.
Lois and Clark - there's an episode in which Mr. Mxyzptlk causes a burp in time, forcing Clark to relive a day again and again during which everyone becomes more depressed and pessimistic. Each time it happens the Christmas tree in the Daily Planet office dwindles until it's just a stalk with a bauble on it.
In the pilot of Friends Rachel makes coffee. Chandler and Joey think it tastes awful, but they politely pour it into the potted plant on the table rather than upset her. Cut to a scene later in the day and Monica has to toss out the now-dead plant.
On Heroes, Mr. Linderman demonstrates his healing power on a wilted orchid.
On iCarly: Carly devises a homemade pesticide for her science project and tests it on Spencer's healthy tomato plant. Said plant smokes profusely and withers instantly. Carly exasperatedly deems herself (and later Spencer) as "The Plant Murderer".
Intentionally used on Hogan's Heroes. Colonel Hogan wants to keep convincing Klink that a killer is after him, so he laces the kommandant's tea with what's probably a powerful herbicide and serves it to him—then, at the last moment, notes that the tea might be poisonous and pours it into Klink's office plant instead. The plant dies dramatically and Klink believes Hogan's story.
In the Bottom live show, Richie dumps a cup of tea that has been laced with goat poison onto a nearby plant. The plant gives off smoke and wilts instantly.
Dilbert featured an arc where Wally's potted plant becomes the waste receptacle for his coffee dregs. Dilbert later suggests to him that he switch to decaf; the next panel shows a giant tree growing out of the office building.
Ace Attorney: It's implied that Ema did this to Phoenix Wright's plant. Though seeing as it is still around in the 4th game, and is implied to be the same plant, it survives.
In the pilot for Batman Beyond, we only see the full effects of the illegal nerve gas on a plant. Human and cattle subjects are also displayed, but what happens is only implied to be horrible through villain reaction shots.
The tiny little Death Omen pine tree from The Nightmare Before Christmas. It eventually bursts into flames, causing Sally to seriously question whether Jack's great Christmas takeover plan is such a good idea.
Done for laughs in Teen Titans by Beast Boy when the bathroom was occupied.
Inspector Gadget – MAD assassins try to bump off Gadget by poisoning the hors d'oeuvres at a party he’s attending. Brain gets rid of them by dumping them in a nearby potted plant, which promptly wilts and dies.
In Futurama whenever Bender tries to cook the Planet Express crew dumps the food into a plant, lampshaded by Bender when he asks "How come the plant only gets sick when I cook?".
One S2 episode of Winx Club had Bloom experimenting with her recently discovered healing powers, using some plants as test subjects. However, since the book she had gotten from the library had been planted there by an evil spy, it caused the spells she used to cause one of the plants to burst into fire, and another to turn into a monster. This trope is also inverted when in S4 Ogron, the leader of the Wizards of the Black Circle steals the gift of life which could be used to bring a dead person back to life and uses it on a dead flower to prevent the Winx from using it to revive Nabu, who had just sacrificed himself to save the Earth fairies from the Dark Abyss that the Wizards of the Black Circle had created.
In "Hand in Hand" on Kick Buttowski, Kendall, disguised as Gunther, releases a burst of flatulence that not only creates a great wind, it causes several plants to blacken and wilt instantly.
Subverted and inverted in an episode of Darkwing Duck. Bushroot is out to make himself another plant friend. He comes up with a promising goop that seems to work. Then it gets on Gosalyn. Then Darkwing tests the goop on a smaller plant then the one Bushroot used... and the plant dies within minutes. Apparently, the goop is deadly within a day or two. But Darkwing announces that he did find a cure... although how he figured out that cure from testing on plants is never explained. The cure is a hot bath with lots of soap.