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Some fandoms are very often used for fusions and are defined more by their fusion potential than by fannish activity in-universe alone; His Dark Materials is a good example, with whole livejournal comms being devoted to the genre.It's a little easier to talk about this type of thing in comics fandom, where there's a clear-cut difference between a crossover and an amalgam-- every so often DC and Marvel will get together and do an "Amalgam" comic, where two universes are squished together resulting in something like Sparrow, who is a squished-together version of Robin and Jubilee.) Anyway, that's what these stories should be-- not crossovers where Angel or Jim Ellison or Horatio Hornblower or Remus and Sirius suddenly discover the existence of Atlantis, but one where they've been there this whole time, as Marines, or scientists, or Athosians, or whatever. Where they've become part of a team, just as they are in their original fandoms. 
Popular Fusion Types
Fusions often borrow a setting or an element of canon, and ignore everything else from these fandoms; canon knowledge (sometimes even on part of the writer) is rarely necessary.
- There are many stories in which characters are students at Hogwarts (often prompted by an idea about which House a particular character might attend.)
- Jedi and Sith in the Star Wars universe
- Anne McCaffrey's Dragonriders of Pern universe
Borrowed Canon Elements
- Characters exist in a world where humans have dæmons from His Dark Materials
- Superhero or mutant powers, similar to the X-Men
- Character X turns out to be a Highlander-style Immortal
- Slayers & Watchers from Buffy the Vampire Slayer are imported to other universes
- Characters X and Y have a fanon Sentinel-Guide soulbond from The Sentinel. (Often these take place in a darkfic AU where the existence of Sentinels and Guides is publicly known, and Guides may be unwillingly coerced into their role as soulbonded sidekick.)
- A character is under an obedience curse, as in Ella Enchanted
- Magical abilities like those of The Curse Workers
- Jaegar pilots and kaiju from Pacific Rim
Same Actor Fusion
A Same Actor Fusion is like a Same Actor Crossover, but rather than having two characters in different canons who are played by the same actor meet, they are combined into one. These stories usually include a fusion of other canon elements such as setting as well as characters.
- This fusion began being drawn and written when it was announced the Benedict Cumberbatch had been cast along side his Sherlock co-star Martin Freeman as the dragon Smaug in The Hobbit. The portmanteau names "Smauglock" and "Johnbo" refer to the Smaug/Sherlock fusion and John/Bilbo fusion characters respectively.
- Drawing characters from other fandoms as ponies from My Little Pony: Friendship is Magic
- Night Watch, by Brighid. Sentinel/Batman fusion with Jim Ellison as head of EllisonCorp during the day and vigilante at night.
- Scheduled for Termination, by Dolimir. A Supernatural/Sarah Connor Chronicles fusion. 
- Inclination by jacquez where Blair is a straight Vulcan Guide with his own secret reasons to want to bond with Sentinel Starfleet Captain Jim Ellison.
- A Heartbeat At My Feet, by Kellifer_fic. A Supernatural/His Dark Materials fusion in which Sam and Dean have dæmons. 
- There Is No Gene, by T'Mar. A Gattaca/Sentinel fusion. 
- X, by trinityofone, in which the characters of Stargate: Atlantis have the mutant powers of the characters from the X-Men Movieverse, with John Sheppard taking on Rogue's superpowers, Teyla Emmagan taking on Mystique's, and so on.
- Blade Runner by newkidfan, a vid merging Merlin characters with the Blade Runner universe
- And All The Stars Burned Bright, by mintcloud. Transplants the main characters of the British detective drama The Inspector Lynley Mysteries into the Star Trek universe during the Dominion War, with Thomas Lynley as Captain and Barbara Havers as his first officer.
- Behind the Sea (Alternate Universe version) (link), by airgiodslv, places bandom characters in a universe based on seaQuest DSV.
- Across Dark Waters by Zimraphel is a relatively early (2003) example which fuses Silmarillion characters with Greek myth
Same Actor Fusions:
- The Lonely God by inukagome15, Sherlock Holmes/Iron Man fusion in which Loki gives Sherlock Holmes a golden apple for selfish reasons. (Holmes/Watson, Steve Rogers/Tony Stark)
Sometimes major characters in their original universe become minor characters in the new fused universe:
- Stay Left, by skoosiepants, has HP characters as minor players on SGA's Atlantis.
- Poptarts in Atlantis, by torch, puts members of the boyband 'N Sync to work on SGA's Atlantis.
- The Hammond Affair, by queensheep, tells a new story in a Jurassic Park universe inhabited by bandom characters, and features Alexis Hammond as a minor character.
Fusions offer many possibilities for humor:
- The Dark Side, by astolat, is hilarious -- Rodney plays the crankiest Jedi and John Sheppard is the prettiest Sith.
- Truth, Justice, and Rodney McKay, by siriaeve, is bizarrely charming fusion where Rodney plays the Lois Lane part, and John is both Superman and Clark Kent, I mean, Sheppard.
- Merlin/Calvin and Hobbes fusion comic strips by shiyasim
- strive seek find yield by waldorph, a hilariously successful crackfic fusion between Star Trek and The Young Victoria, with Spock in an AU version of the role of Queen Victoria and Kirk in the role of Prince Albert.
- RatCreature. How to construct Alternate Universes that work as fanfic. Originally posted to FCA-L on 28 January 2001. (accessed 6 November 2008)
- Atlantis Amalgamated: the fusion universe Accessed November 6, 2008
- NEW CHALLENGE: ATLANTIS AMALGAMATED" Accessed November 6, 2008
- "The thing is, AUs aren't copy/pastes of movie transcripts. Can an author lift dialogue? Sure. Lift scenes and circumstances? Absolutely. Does an author have to explain the characters and how they feel in that situation? Yes. [...] And that's the the thing about AUs: they're work. You have to know what you're saying about the characters and there has to be something deeper there. screamlet and leupagus and I have spent hours talking about it over the course of writing Legends and Spoctoria and even Dr. Princess -- these characters don’t exist in vacuums, and even when you put them in space operas, they're still them with defined character traits and baggage. You have to respect that and then tell the story from there. [...] An AU is not an excuse to write OOC. Otherwise you're just parroting back the film (and I can watch that)." from ON THE SUBJECT OF MOVIE AUs/FUSIONS (No, Really, Apparently This Needs To Be Said), essay by waldorph, 11 January 2011. (Accessed 11 April 2011)
- ääärrr by Sadynax
- Brighid. Night Watch. Posted 4 September 2000. (Accessed 7 November 2008)
- Dolimir. Scheduled for Termination. Posted 29 August 2007. (Accessed 7 November 2008)
- Inclination, by Jacquez. Posted 27 May 2001. (Accessed 7 November 2008)
- kellifer_fic. A Heartbeat At My Feet. Posted 22 January 2008, accessed 07 November 2008
- T'Mar. There Is No Gene. Posted 23 October 1998. (Accessed 7 November 2008)
- "X", posted 16 August 2006, accessed 06 November 2008
- inukagome15, The Lonely God, accessed 06 April 2014
- skoosiepants. Stay Left, posted 17 December 2006, accessed 06 November 2008
- Poptarts in Atlantis, accessed 06 November 2008
- Astolat. The Dark Side, posted 27 July 2006, accessed 06 November 2008
- Siriaeve. Truth, Justice, and Rodney McKay, posted 21 January 2007, accessed 06 November 2008