Cease and desist letters
From Fan History Wiki
There is a questionable legal status for fan fiction. As of 2007, no one has yet to go to court in any country to finally challenge the material's legally ambigitious status.
But that doesn't stop intellectual property holders or individuals from trying to control fan fiction based on their material. The means of doing this fall into three general categories: asking a writer or archive to remove fan fiction based on their intellectual property, creating a licensing policy for fan fiction writers to play in their universe or send a cease and desist letter demanding that certain actions be taken.
Cease and Desist Letters
Fan fiction traditionally has two components. One is the media side of fandom and the other is the real person fic side of fandom. To date, there are only four known cease and desist letter sent regarding real person fic. This letter was recieved by FanDomination.Net on March 13, 2003 for materials pertaining to Andy Pettite, a baseball player. The letter demanded that libelous materials be removed. Another one asked for character journals featuring Canadian Idol contestants be removed. A third involved Ohio State University women's basketball fan fiction be removed with other real life consequences for the person. A fourth involved AdultFanFiction.Net and an NSync story involved one of the band members being written as a minor.
The media side of the fan fiction community has not fared as well. There have been numerous letters sent in a variety of fandoms.
The Highlander fandom was not one to escape threats of legal action. In 1996, a Highlander fanzine recieved cease and desist letter. (Farmer, V. (1996, October 30). Having my say. Message posted to alt.tv.highlander)
Anne McCaffrey had been aware, based on interviews, of fan fiction since 1985. As fan fiction moved on-line, she, in consultation with lawyers, created a licensing policy for people who wished to write fan fiction in her universe. On her official site, this policy was explained as one required because of contracts related to Anne McCaffrey's books having been turned into video games. Given all this, it does not come as a surprise that in 1997, a Dragons of Pern fan fiction site recieved a cease and desist letter from McCaffrey's legal representatives.
One community hit especially hard was the Anne Rice fan fiction community, based on Usenet. In 1999, Anne Rice threatened a number of fans with legal action.  This was followed up with cease and desist letters being sent to fan fiction sites and, in 2000, a personal statement being published on her website saying that she was hurt by people writing fan fiction based on materials. This all culminated in 2001 with FanFiction.Net recieving a cease and desist letter.
On November 23, 2003, Duck's Fan Fiction Archive, a Buffy: The Vampire Slayer fan fiction archive, recieved a cease and desist letter.  There was some controversy regarding this as the show's creator had been an avid supporter of fan related activity in his fandoms.
A series of Fan-dubbings of the "Knowing is Half the Battle" segments from the end of the animated series "GI Joe", received a cease-and-desist letter from Hasbro, who made the original toys that the cartoon was based on and owned the rights of the characters, but by the time they wrote that letter, the videos had already been downloaded and reposted all over the internet.
The Caroline in the City fan fiction community, though small, was not spared from recieving legal threats. One fan fiction site recieved a cease and desist letter from CBS in 2004. (Chilling Effects) That same year, sg1archive.com, a Stargate fan fiction archive, received a cease and desist letter.
On July 12, 2004, MediaMiner.Org received a cease and desist letter requesting that a fiction by an author under the username "NyliramLlessur" be removed. This letter was sent by a Silhouette Books representative who alleged that the story was nothing more than the novel "Guilty Secrets" by Virginia Kantra with the names changed out and replaced with the names of anime characters.
In addition to legal threats which are fandom specific, there have been a number of general cease and desist letters. These targetted multiple sites or were unrelated and yet had an impact on fandom. In 2005, the Motion Picture Association of America sent cease and desist letters to fan fiction sites for using their ratings system. This same year, German lyric sites recieved a cease and desist letter for every song where they have lyrics up. While no German fan fic sites recieved these letters, back lash occurred and sites like FanFiction.Net took steps to ban songfic.
In 2005, a member of the fan fiction community recieved a cease and desist letter from Ohio State University for her NCAA Ohio State University women's basketball femslash. The fan was also kicked out of the Rebounders, the Ohio State University Buckeye's booster club. The university informed the NCAA of her actions. 
Around August 12, 2007, the fan fiction author Meyshi filed DMCA takedown notices in regards to fan fiction authors who sporked/MSTed her work on LiveJournal's deleterius community and God Awful Fan Fiction.  She claimed they violated the copyright in regards to her fan fiction.
Reasons for Cease and Desist Letters
Why do the creators send these letters? There are four major reasons why this is likely.
1. Retaliation in fandom. People get annoyed at other fen and then invite TPTB or harass TPTB in to taking action. Good recent case of this? See SpoilerGate in the CSI fandom. See also the Blake's 7 kerfluffle back in the mid to late 1980s which resulted in at least one fan artist who drew pictures of Paul Darrow's character naked getting a cease and desist letter.
2. Bad publicity. The last round of Harry Potter cease and desist letters, I think that was 2003, were a result of that. It is very likely that the newspaper articles talking up the adult material were why the Restricted Section getting a cease and desist letter. McStories.Com because really well known for their pr0n and got cease and desist letters from DC Comics and others because really, who wants their intellectual property associated with erotica involving mind control?
3. Material being thrust in their faces / Perception that money is being made off their work. This is the case with at least one Star Trek cease and desist letter. It is also the case with a Highlander related cease and desist.
4. Media companies and new technology. Some times, it takes them a while to adapt to new technologies and they react poorly in that period.
- Beckles, T., & Heins, M. A Preliminary Report on the Chilling Effects of "Cease and Desist" Letters. Retrieved April 28, 2005, from http://www.fepproject.org/commentaries/ceaseanddesist.html
- Caplan, D. K. UNAUTHORIZED USE OF TIME WARNER ENTERTAINMENT COMPANY, L.P.'S AND DC COMICS' PROPERTIES. (1998, December 3). Retrieved April 28, 2005, from http://www.mcstories.com/Threat.txt