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Canon (in the context of fandom) is a source, or sources, considered authoritative by the fannish community. In other words, canon is what fans agree "actually" happened in a film, television show, novel, comic book, or concert tour. Specific sources considered canon may vary even within a specific fandom.
The term derives from the theological concept of canon: the foundational texts of a religion, such as the Tao-te-Ching, the Bhagavad-Gita, the Talmud, and the Bible.
While some scholars have argued that Sherlock Holmes fandom was the first to use the word "canon" in its fannish sense, this not quite correct. Their usage popularised, and gave added fannish heft to, an already common way of speaking about given bodies of fiction: "while Morley’s 1934 essay “Doctor Watson’s Secret” called the tales “the canon,” the word was uncapitalized and lacked religious reverberations. It seems simply the term that occurred to the deep-dyed bookman in referring to the literary corpus, as often applied to other, lesser secular works such as Shakespeare. Elmer Davis had already used “canonical” the same way in reviewing Starrett’s Private Life. Morley was Quaker in upbringing, not given to extravagance of religious expression in any event. Not until 1941, in an unpublished memoir about the BSI’s beginnings, did Morley use a religious term: “since the Baker Street Irregulars refer to [Conan Doyle’s] works as ‘The Sacred Writings,’ perhaps he may be nominated ‘The Sacred Writer’” — but he did so as a nod to his old chum Elmer Davis, saluted by name immediately afterwards." (Jon Lellenberg, “The Ronald Knox Myth.” The Sherlock Holmes Journal, vol. 30, no. 2 (Summer 2011), 5358. )
The collective name for a series such as Sherlock Holmes is the Canon (borrowed from religious terminology, because Sherlockian fandom grew out of Msgr Ronald Knox's article on textual criticism of the Holmes story - he meant it as a joking way of suggesting that textual criticism was a nit-pickingly silly way of trying to prove the Bible non-historical, but SH fans ignored the intended point and concentrated instead on the amusing game of applying questions of historical consistency to fiction). 
(However according to Lellenberg's thorough account, Knox seems never to have actually used the term himself: "Father Knox was not satirizing religious rites; he was satirizing German scholarship, a very different thing.")
The word cannon refers to a form of artillery gun and is pronounced the same as canon. Many modern fans have limited exposure to the religious usage, so they use the more familiar spelling, which leads to bemused rants by those who do understand the difference.
Official vs. Canonical
In some cases, a fandom may embrace one work by an author, and yet reject a closely related work as "not canon." An author's works may be considered canon, while statements by the author are often considered to be merely opinion. See Fanon.
Prop Canon is related to physical objects shown in a movie or a TV show, for example college degrees, driver's licenses, etc. Lacking conflicting evidence, prop canon is considered a reasonably canonical source, but occasionally dialog, or later show development may cancel it out. For example, in Stargate SG-1, Jack O'Neill had different birthdates depending on which driver's license was shown, while Rodney McKay on Stargate Atlantis has a certificate on his wall that gives his name as 'Rodney Ingram McKay' which was later contradicted in the episode McKay and Mrs. Miller when his sister said his full name was Meredith Rodney McKay.
Grey canon or gray canon refers to canon that is ambiguous in its canonicity: a detail implied or easily inferred in canon but not confirmed outright; a detail brought up in a creator commentary or podcast but never stated in canon itself. (Essentially, the canonicity of that fact is in a gray area.) An example of grey canon would be the "Previously" segments in Battlestar Galactica, which are not, in fact, previously aired material from an episode. Since the not-actually-Previouslies do not occur within the bounds of an episode, it is not unreasonable to call them non-canonical; but since they affect the episode to which they are attached, it might also make sense to call them part of canon. Another example is the character Billy from Power Rangers, whose surname was never stated on the show but who was referred to on some merchandise (and, years later, on the official Power Rangers website) as "Billy Cranston." Although many fans have embraced "Cranston" as canonical, there are some who do not accept it as canon.
Closed vs. Open Canon
A fandom is considered to possess a closed canon when no additional source material is expected to be forthcoming (there are no upcoming books, episodes, or movies in the series).
By contrast, an open canon would thus be one in which new episodes, books, or movies are being produced.
Canon in Real Person Fiction
RPF has inherited the story tropes and fanspeak of FPF, and along with the woobies and angst and all those first times came a way of discussing and of conceiving of RPF as a form of fanfiction. The terms canon, fanon and AU get bandied about in RPF circles the same way they're used in FPF meta.
While canon in FPF usually refers to the single recognized source for the fandom, in RPF there is no single source, and sources often contradict. Not surprisingly, fans don't agree about what is and is not canon in RPF fandoms, or how important it is to a story that isn't represented as an AU to get all the facts right. All RPF is a balance between the Real and the Fiction, but not all RPF sets the same balance. The sources of RPF canon are many, and not all fans have the time or inclination to research every piece of information available: tweets, convention appearances, TV or movie gag reels, interviews (both in print and recorded), "making of" documentaries, albums (for music), autobiographies, and biographies. And even when the facts (or gossip) are known, fans will disagree about what is appropriate to include as "canon" and what is invasion of privacy.
Writing canon-based RPF has been compared to writing historical fiction where an author is "filling in the blanks of an event that really happened". This kind of story encompasses everything from Sports RPF stories that contain play by play recreations of actual games to Historical RPF which recreates the lives of sometimes long dead historical figures, extrapolating from detailed knowledge and research of the period. Actor and musician RPF also has these sorts of stories where the filming of specific episodes of television shows, parts of films or actual concerts are an integral part of the plot.
The level to which an RPF story is not canon compliant, and the point at which it becomes an AU, is open to debate. At the extreme end of the spectrum, stories that place real people in scenarios totally removed from their actual lives, stories where the members of My Chemical Romance are on a spaceship or where J2 are bullriders are obvious uses of the real characters in completely non-canon settings. While some aspects of their canon selves might come along for the ride, no one thinks the story is supposed to represent their real lives.
The less obviously non canon–compliant story is the one where My Chemical Romance members are still musicians and J2 are still actors, perhaps even doing many things the real people have actually done, but the desire on the part of the author for perfect detail, or their willingness to use non–celebrities in supporting roles, may push the story away from true canon compliance. This distinction is harder to draw, and different fandoms have different cultures that determine where that line is.
To some extent all RPF, and all historical fiction as well, contains elements of fiction mixed in with the reality of the characters. In RPF though, the author may be setting the story in a simulacrum of the person's real milieu—describing some semblance of a television show studio or tour bus—but was never intending to realistically portray that person's life. In these stories, the use of fanon in place of canon is often intentional. In other cases the author chooses not to learn the difference between the two, either because they don't want to research every detail of their characters real life progenitors, or they don't think they should.
Canon in Pop Culture
T-Rex of Dinosaur Comics once proclaimed several events in his life to be non-canon, including "any event in which I was embarrassed." 
Rejecting Canon and Dealing With Canon Inconsistencies
- Reset Button
- SND, a Beauty and the Beast (TV) term used to describe fanworks that rejected the third season of that show
- lots more
From the influential 1973 supplement to the Star Trek Concordance:
NOTE: T.S.I. stands for "Third Season Inconsistency." There were many ways we could explain away careless handling of the third season scripts, but a few of the more blatant blunders were just too much for even our fertile imaginations to make up excuses for! When we could offer a reasonable rationale for a mistake (such as fatigue, excitement or other reason for getting a Star Date mixed up, or other blunder) we did so; the nitpickers can have fun finding those. But a few we just gave up on, and labeled as T.S.I.
Mistaking Differing Characterizations For Non-Canon
Some fans feel that canon also extends to characterization and not just the facts or events that take place in the published novel or on screen. The two are so intertwined that a character who behaves "non-canonically" is also considered to be based on "illogical characterizations" that are not supported by the source:
Decades ago, Devra Langsam (coeditor and publisher of SPOCKANALIA, the first Star Trek fanzine, beginning in 1967) codified this in what came to be known as "Langsam's Law." In an essay published in WARPED SPACE 50 (1984, T'Kuhtian Press), Paula Smith described it thusly: "In writing media-based fiction there is a special caveat: Langsam's Law, or, 'Don't Make Him Say That.' Don't make an established character do or say something out of line with his established character, or if you must, give good, solid reasons why. If you must write a Darth-Vader-is-really-a-pussycat story, explain in the story why he also strangles crewmen when irked." And the debate has raged ever since. For my own part, I initially was somewhat startled to realize, upon reading my first fanzine those many decades ago, that other people could and did interpret these characters somewhat differently than I did. After a while I concluded that there was a continuum of logical characterization--always demonstrably rooted in canon--along with the who-the-fuck-*are*-these-people "interpretations." As far as I can tell, these are based on projection, wish fulfillment, and/or what I call "spackletext" (as opposed to genuine subtext) from writers (well, story posters, at least) who want the characters to meet their specific desires in emotional/physical/therapeutic gratification and are completely oblivious or simply uncaring as to how that is achieved. 
I don't understand how an otherwise intelligent and talented individual[s] could invest so much energy in "Official Star Trek" as if that's what counts. I don't care what Paramount does. I'll use what I can use and through away what I can't, I still have my own mind and imagination. The zines still exist and alternate universes are infinite. Relax. Forget about Roddenberry's wrongs whatever they may be and Bennett's treasons. From the point of view of the active fan writer, they have no importance. We created ST fandom as it exists now, and we have total control of ST in our zines. Let them go to Hades in a trans-warp drive hand basket even if it contravenes the laws of physics and continue to do your own thing in ST. 
I used to stick to canon religiously. Now, I just say "screw it" for Trek... The bottom line is that I'll stick to canon religiously, until the show itself gives me cause not to.... what's the point of sticking to canon? If you want to, sure, but we're already breaking the rules just by writing trek at all. If canon makes sense within the context of your story, keep it. If not, wave bye-bye. 
Who cares!? Canon sucks! Canon sez Jim Kirk, the jewel in the crown of the ST character universe, is now dead. Obviously, canon is for people with no wits or taste. You don't kill off the hero...anybody who has any sense knows that.You know who IS dead? Gene Roddenberry, that's who. He can't keep control over Star Trek anymore. ST belongs to the world and the fans now. As for me, I'm in the Nexus with Jim Kirk. DO NOT DISRUPT!
'Canon' in the sense that I use it is a very important tool. It only gets muddled when people try to incorporate licensed products into 'canon' – and I know a lot of the fans really like to do that. Sorry, guys – not trying to rain on your parade. There's a lot of bickering about it among fans, but in its purest sense, it's really pretty simple: Canon is Star Trek continuity as presented on TV and Movie screens. Licensed products like books and comics aren't part of that continuity, so they aren’t canon. And that's that. Part of my job in licensing is to keep track of TV and Movie continuity, so I can help direct licensees in their creation of licensed products. It gets a little tricky because it's constantly evolving, and over the years, Star Trek's various producers and scriptwriters haven't always kept track of/remembered/cared about what's come before.
...the authority of canon is endowed not by its creators, but by its fans. In forming canon, fans choose the pieces of canon that they like and discard the rest, and what’s really remarkable about this process is that it is both individual and deeply, deeply communal. We have our own idea of canon, but we also debate what should be in the canon and what should not. In fact, original authors take part in the same debate. At the end of long running series, they often provide definitive pairings to quash fandom speculations.
In its original context, canon refers to religious texts like the Bible, itself subject of endless debates over the meanings of its words. In a church right now, the Biblical canon is being contested.
That is because “canon” is a contradiction in terms, and it cannot exist without being contested. It is considered “authoritative,” but canon’s very power and authority become the grounds for questions, and challenges, and doubts. The more we adhere to canon and the more seriously we take the words on the page, the better we see the cracks and the more questions we ask.
The complex relationship that fans have with original authors mirrors this anxiety. These original authors are sometimes referred to as The Power That Be, or simply Creators, and their pronouncements are Words of God. For the major religions, their gods are either dead or non-living beings, communicating with their flocks only through cryptic thousands years old manuscripts, but for many fandoms their gods are talking shit on Twitter dot com, after which discovery it becomes significantly harder for fans to take them seriously.But gods only exist if they are worshiped, and canon is made not by creators but by fans. The “canonical” versions of ancient fairy tales may be dark in their first tellings, but the versions anyone cares about are the Disney ones, which hold more cultural power. Culture, in case we forget, is a social activity. There is no one true canon; it is an amalgamation of all our ideas about what it should be. Canon is also constantly changing, waiting for the next person to take it, to shape it, long after the original author has written the last word. 
- Tiny Marshmallows Want to Be Free by Mer (1999 or early 2000s)
- Canon? Canon? What is canon? (was: Gary Mitchell and Contradictions in Canon & Fanfic), Archived version -- Canon? Canon? What is Canon, Archived version -- Canon? Canon? What is canon? (was: Gary Mitchell and Cont..., Archived version, a March 2000 discussion on alt.startrek.creative.erotica.moderated
- Why bother writing in a fandom if you want the characters to be significantly different? (2003)
- Canon/fanon, Archived version by Jane Davitt (2004)
- More Than You Ever Wanted to Know About Canon and Fanon, Archived version by Melusina (2004)
- Canon canon canon starts with C, Archived version (Jan 2005)
- Canon, Music Theory and the Fandom, Archived version (Jan 2005)
- Life After Deathly Hollows (2006)
- Fandom Meta : The Two Sides Of Canon, Archived version by Nikki (April 2006)
- Canon Versus Fanon Versus Authorial Intent by Merlin Missy (2007)
- Re: Catching Up With Past Anons, Archived version - fail_fandomanon discussion about what is good use of canon in RPF fic (2013)
- Creating Headcanons: Everyone Does It (2015)
- Do Characters Belong to Their Fans or Their Creators?, Archived version (2015)
- Captain America and Bucky are Just Friends (2015)
- Do you know when "canon," like as a concept, became like a standard nerd thing? answered by vintagegeekculture (2017)
- comments by Ruth Herman in Horizon Letterzine #3 (August 1992)
- copperbadge. etymological discussion of canon vs cannon, posted to Dreamwidth 9 January 2013. (Accessed 2013-04-17)
- emily_shore. Two kinds of RPF, posted February 11, 2009. (accessed March 25, 2010.) archived.
- mrs_leary in bradleycolin—Crossing the line in RPS..., posted September 14, 2009. (accessed March 25, 2010.) archived.
- T-Rex oh man, last night was so non-canon April 06 2004. Accessed October 4, 2008.
- "Don't make him say that" goes back as early as 1972 in Fan Writing Panel or Don't Make Him Say That!, printed in Masiform D 3 in 1973.
- klangley56 commenting in Will the real characterization please stand up?, dated May 29, 2007; accessed Feb 8, 2011; WayBack Machine.
- from. K/S & K.S. (Kindred Spirits) #11
- comment by Jessica Krucek at Fan Fiction -- Why?, September 29, 1996
- comment by Laura Goodwin at Canon sucks! (December 26, 1998)
- comment on TrekBBS at The History of Defining Canon (accessed February 2, 2021)
- The Fandom Meta Blog, Archived version, post by Erica (July 2018)