A standard post-9/11 plot for American television. A One-Shot Character is introduced who is Middle Eastern and Muslim. The majority of the cast welcomes this new character with open arms, except for one. He's convinced that this new character is a terrorist, and will do whatever it takes to show the rest of the cast that his suspicions are correct. In doing so he invades the new character's privacy, and eventually learns An Aesop about being considerate of other cultures.
Alternately, a character is mistaken for a terrorist while acting suspiciously in an airport or on a plane. Most of the time it's a misunderstanding. Something or other will be Mistaken for Evidence (for example, the suspect will say something like "This party is gonna be the bomb!").
Unfortunately, this is Truth in Television (Real Life examples might double the page length or more). A number of people on airline flights have been discriminated against, including being forced off the plane, because the other passengers or pilots panicked and thought they were terrorists just based on their appearance or misunderstood actions (and there are reports of some who invoke this trope to test the waters or make it harder to find the ones with bombs). Sikhs and Orthodox Jews have to deal with this too.
This trope can be viewed as an updated version of Mistaken for Spies, reflecting how the "enemy" changed between the Cold War and The War on Terror.
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A variation occurs in a Dork Tower strip with a "radical" "extremist" "black panther" named Huey. He's a white guy wearing a black furry panther costume.
Happens in the November 2011 issue of Knights of the Dinner Table when the group plays a real-life based Zombie Apocalypse game of Screams of Kachuloo. Brian's frequent Internet searches for bomb-making and the layout for the local mall (for the game) throws up red flags with Homeland Security. A more experienced member of the department sees that the address is in gamer-heavy Muncie, Indiana and calls off the team. They've been burned there before many times...
Happens to a young Arabian man in a issue of Power Girl as the plane he is in starts to fall from the sky as he uses his super powers to save the plane and its passengers. He mentions that the reason he never use his powers before was because he knew they would consider him a terrorist.
Films — Animated
In Beavis and Butt-Head Do America, Dallas Grimes hides a dangerous neuro-toxin in the lining of Beavis' shorts with the intention of retrieving it in Washington. When FBI agents realize the two have it, they're automatically branded the most dangerous criminals on the planet. Despite the fact that they have no idea they had it and they keep attacking the casing.
Films — Live-Action
In Harold & Kumar Escape from Guantanamo Bay, we see a POV Shot from a little old lady on the plane and Kumar looks like a terrorist - turban, beard, Evil Laugh. Then he lights up a bong in the restroom and people think he's got a stick of dynamite. He even says "it's only a bong" and people mistake him for saying "bomb."
My Name is Khan features a main character named Rizwan Khan, a Muslim American with Asperger's Syndrome living in post 9-11 America. He says to another character that he wants to tell the President, and the people, of the United States that his "name is Khan and that [he] is not a terrorist." When he repeats this to himself in a crowd gathered to meet President Bush, he is arrested, imprisoned, and tortured as a terrorist suspect. A "Funny Aneurysm" Moment occurred when Shahrukh Khan, the actor who played Rizwan was detained by Immigration offers at Newark Airport on August 14, 2009 and questioned for two hours.
Invoked in Crank. Chev Chelios gets revenge on an obnoxious taxi driver by dragging him out of his vehicle, then pointing at him and yelling "Al Qaeda!" Everyone in the street immediately dogpiles the man and beats him up.
In the 2008 film of Get Smart, when Maxwell is trying to scrap gum off his shoe with a match the plane passengers mistake it for a shoe-bomb. He says it's just Gum which is misheard as Gun.
In Flightplan, Kyle Pratt mistakenly accuses a Middle Eastern man of kidnapping her daughter (although to be fair, his being Middle Eastern wasn't the only reason she thought he was guilty). He is later shown to have nothing to do with the girl's disappearance.
In The Dictator, Admiral-General Aladeen and his minion have an innocuous conversation while on a helicopter tour of New York, but the various snippets of English words they use (like miming the explosion of fireworks while talking about the Statue of Liberty or talking about the "Porche 911 2012") convince the tourists that they're terrorists. Which raises the question: Can a character be "mistaken" for a terrorist if he does actively aid and abet terrorists?
Chillingly subverted in James L Grant's short story The Last Flight: An Indian airline passenger is harassed continually before and during his flight, while the blond, blue-eyed, All-American guy in the seat next to him...
Live Action TV
Law & Order played with this: a family of Italian Americans considered their son's Muslim girlfriend's family potential terrorists. The girlfriend's family thought of her boyfriend's family as Mafiosos. Both lovers end up being murdered.
Another episode had two detectives invoke this trope intentionally on a pair of uncooperative Iranian nationals who refuse to cooperate with an investigation (they happen to work for the Embassy and can't be forced to answer questions or charged for impeding). The police resort to basically planting a camera filled with what would appear to be photos scouting a target for a terrorist attack in NYC. The District Attorney is not amused when he has to deal with the fallout from the State Department over the matter, but he and the police officers involved never face any lasting consequences over the incident.
There was a Degrassi The Next Generation episode where Hazel was harrassing a Muslim girl, even going and telling her to her face "Terrorist chic? So not in," in reference to her hijab. Paige calls her out on it, and she ends up prime suspect when someone vandalizes the Muslim girl's locker. Turns out Hazel is herself Somali and Muslim, and she was doing it precisely for this reason.
30 Rock: Liz Lemon grasses up an Arab man to Homeland Security when she glimpses maps on the wall of his apartment and sees him running through an obstacle course. Turns out he was in training for The Amazing Race.
An episode of Wings had a few of the guys taking the plane for a trip only to end up landing in the middle of a cornfield. At one point Antonio (played by Lebanese-American Tony Shalhoub, though the character is Italian) goes exploring the field to look for help and comes back with the farmer behind him... with his hands raised while a shotgun is pointed at him.
Antonio: Joe, please explain to the nice man with the gun that I am not a Libyan terrorist.
From the first episode of Little Mosque on the Prairie Amaar is talking to his mom over the cellphone at the airport. With this dialogue, it's somewhat understandable they were mistaken:
"I don't care if dad thinks this is suicide. I'm on a mission from god. It's not like a dropped a bomb on him"
Without a Trace, "In Extremis." A Saudi Arabian doctor goes missing, and a lot of people automatically assume he's a terrorist. As it turns out, some of his acquaintances are, but he's trying to stop them. He's killed by a FBI sniper at the end of the episode as soon as they get a clear shot. He was heard talking about blowing up a building by a passing woman, but he is actually talking about how the home stadium of the sports team he's talking about should be demolished because they never win.
24 has two rather tragic examples on Day 2. Reza Nair is the biggest example - CTU initially suspects him of financing terrorist operations, although it turns out he's being framed by his white, blonde, all-American fiancee, who turns out to be the real terrorist. She murders Reza when he finds out. Later in the season, Yusef Auda is an intelligence agent from the Middle East who initially seems like an untrustworthy character but ends up as a fairly awesome ally for Jack Bauer... only to get beaten to death by angry racist Americans who do, in fact, mistake him for terrorist.
In an episode of Titus the titular character was on a plane with his family after his mother's funeral. Mimicking a real life epiphany Christopher had years earlier, he caused a commotion that worried the other passengers. It didn't help when over-indulgent Dave came out of the bathroom with a towel wrapped around his head and Tommy on his knees shouting "Allah" "a la king" (he was correcting a steward's grammer regarding a chicken dish).
Cami from Bones has freaked out over the suspicion that Arastoo is a terrorist twice. Despite knowing he has served as a translator for the US Military in Iraq. The first time her fear was a little understandable, but the second after she supposedly learned her lesson from the first?
In an episode of Chuck involving Chuck choosing new Intersect agents, one of the candidates looked Middle Eastern and had a large beard, and also happened to be an explosives expert. He signed up to be an Intersect agent because was not happy about being constantly assigned to be The Mole in terrorist organizations and was sick to death of being surrounded by nothing but sand all the time.
Subverted when he actually turns out to be a traitor and working with the terrorists.
One of LOST's many flashbacks showed Sayid being investigated by airport security because he is a Middle Eastern man who briefly left his bag unattended. Fortunately, the matter is cleared up quickly and he is cleared of any suspicion. Interestingly, another flashback revealed that at one point he was part of a terrorist cell but was actually The Mole for a US-Australian anti-terrorist task force. As a former Iraqi Republican Guard member he had the perfect credentials to infiltrate such a cell and the US government offered to reunite him with Nadia if he helped them stop a terrorist attack in Australia.
JAG has an inverted example predating 9/11. In 6th season episode "Valor", Sergeant Joan Steele was found with terrorists attempting to sabotage a US warship in the vein of the attack on the USS Cole. It is unclear whether Steele was kidnapped and succumbed to Stockholm Syndrome or was a Military Maverick on a mission of her own trying to stop the terrorists. It turns out to be the latter, as she was killed in an explosion stopping them.
On The Mindy Project in the episode "Harry & Mindy", Mindy (who is Indian) reveals that every year on Valentine's Day she goes to the Empire State Building to hope that she meets that special someone. She walks around the line to go in taking notes. The building security interrogates her and assumes that she plans to blow up the building, because of her ambiguous answers that are actually about romance. She doesn't catch on until Homeland Security walks into the room.
Mindy: I'm here to meet that special someone, and when I do, we're going to go to the top and then BOOM! Fireworks.
During their 2003 Yanqui U.X.O. tour in the US, this happened for real to the band Godspeed You! Black Emperor when they stopped for fuel in Ardmore, Oklahoma. The station attendant working that day assumed they were terrorists, and got another customer to call the police. The cops were suspicious of the band due to their possession of anti-government documents and photos of oil rigs, communication towers, etc. After running a background check, all was well and they were released. The band sometimes joke about the incident at shows.
Maybe it's a Post Rock thing, as Explosions In The Sky were also once mistaken for terrorists, owing to the extremely unfortunate coincidental timing between the release of their album, Those Who Tell the Truth Shall Die, Those Who Tell the Truth Shall Live Forever and the September 11th attacks. You see, the album, conceived and recorded well before September 11th, has a picture of an airplane captioned "This plane will crash tomorrow" as part of its cover art. This, coupled with rumors that the album was released on September 10th (it was actually released in late August,) and probably not helped by the fact that their guitarist is of Pakistani heritage, was enough to get their bassist briefly detained at an airport as a potential security threat.
This was pretty much Muhammad Hassan's defining character trope. It didn't help matters when he started doing things like summoning men in ski masks to choke people with piano wire.
Russell Peters has a routine where he describes his experiences of being an Indian-looking man trying to fly right after 9/11. He describes a man freaking out and screaming "OH MY GOD, NO!" when Russell attempts to pull something out of his bag.
Fortunately he was released when their caucasometer picked up his Viking heritage.
Inverted in Harry Potter Comics. Three Muslims at the Ministry of Magic are left alone by everyone, except one of the villains. However, as it turns out, they ARE terrorists and blow the place up. One of them has a Heel-Face Turn later, though.
American Dad! episode "Homeland Insecurity" when ultra-conservative Stan Smith assumes the new Iranian neighbors are terrorists. He turns his house into a detention camp where he puts the Iranians and eventually all of the other neighbors into captivity.
And a bit later, Stan mistakes himself for a terrorists when he finds his car crashed into the town's energy plant (it was actually Roger who drove it).
South Park episode "The Snuke." Cartman automatically assumes that a new boy at school is a terrorist because he's Muslim. While there does turn out to be a terrorist plot going on in town, it is in fact it's a Russian working for the British.
The Simpsons episode "Mypods and Boomsticks". Similar to South Park's "The Snuke", Homer assumes Bart's new Muslim friend (even sharing the same last name as you-know-who) and his parents are terrorists.
Also played for laughs in the episode "Midnight Rx", where Homer takes Ned Flanders and Apu across the border to Canada to pick up some medication. On the way back, Apu takes a sip of some very hot coffee, and burns his tongue. Ned then gives him a wet towel to wear around his head, which, combined with Apu's now unintelligible screams, gave the wrong impression to the border guards.
This is the point of "Homerland", where Lisa suspects that Homer has been brainwashed when he starts acting polite, resists pork and beer, is seen praying faux-Muslim and takes a mysterious device in to the power plant. When Lisa and the FBI confront him, it turns out Homer was turned by eco-activists who convinced him to go vegetarian, went through an alcohol detoxication, was doing exercise on a rug they gave him (his "prayer" was "Ow, this rug hurts my knees"), and was doing a non-violent attack on the power plant (stinking up the plant so badly that nobody would go there anymore). The plan failed because the plant doesn't have air conditioning.
One episode of Minoriteam featured the group going on a trip in their civilian identities. The Indian Dave Raj, however, slept in, and was forced to transform into his super-powered self, Nonstop, and hop on his flying carpet to get to the airport on time. Nonstop wears a turban and has a long beard. You can probably figure out the rest on your own.
The King of the Hill episode "The Accidental Terrorist", Hank recruits a trio of teens to get back at an Honest John's Dealership for ripping him off, but when they blow up several cars, Hank is blamed because he was the only one who showed up in the security footage (due to the teens wearing black clothes and lying down on the pavement as camouflage).
The title character of Archer naturally assumes that a turbaned Middle-Eastern man is the suspect (just moments after dismissing the German with the eyepatch as "way too obvious"). It's pointed out that the guy is a Sikh.
Archer: "Oh, so if he's not a Muslim he just gets a pass? Well, that's called profiling, mother, and I don't do it. "