Stargate

Stargate SG-1 and its spin-off, Stargate Atlantis, are two continua that are part of the same canon universe. They are based on the 1994 film Stargate.

Stargate SG-1
Exceedingly fast interstellar travel in this 'verse is possible with the use of 'Stargates', ancient devices made by aliens, which form a network between various planets in various galaxies. The story follows SG-1, a team of military explorers who use the Stargate to travel to new worlds, finding new technology and making contact with aliens in order to defend against a parasitic alien race known as the Goa'uld. In later seasons, the Goa'uld are replaced as the Big Bads by the Ori. The replicators, which are robots comprised of small individual building blocks and look remarkably like evil insectoid erector set models, are another recurring enemy.

There is a remarkably thorough Stargate Wiki that includes all the information you could ever want to know about the original movie, each of the three spin-off shows, the spin-off movies, and all other sources of material such as games and books that contribute to Stargate canon.

SG-1
The original members of SG-1 were:


 * Jonathan "Jack" O'Neill (Richard Dean Anderson)
 * Daniel Jackson (Michael Shanks)
 * Samantha "Sam" Carter (Amanda Tapping)
 * Teal'c (Christopher Judge)

Carter and Teal'c are the only two who remained regular cast members throughout all ten seasons. O'Neill was replaced as team leader by Cameron "Cam" Mitchell (Ben Browder) in season 9, though O'Neill remained a recurring character. Jonas Quinn (Corin Nemec) took Daniel's place during season 6 due to Daniel being dead (not for the first time), and left when Daniel came back.

Vala Mal Doran (Claudia Black) notably had a recurring role in seasons 8-10; "notably" because Claudia Black and Ben Browder were previously co-stars in Farscape, which had been canceled. (If the Sci-Fi Channel was hoping this move would win over estranged Farscape fans, they were only partially successful.) Their presence led to a Farscape crossover spoof in the season ten episode "200".

In badfic
Daniel Jackson is a frequent target of rape!fic and of slave!Daniel fics. The DADT and chain of command issues are very frequently blatantly ignored to allow Jack and Daniel or Jack and Sam (either couple) to be openly dating or even married.

While rare, Jonas fic usually includes either him being raped by OC's (often random marines), or being abused physically and/or verbally/emotionally--often by other members of SG-1. Although the other members of SG-1 were somewhat hostile toward him at first, because of his actions around the time of Daniel Jackson's death, they were never outright abusive, and he was eventually fully accepted as a member of the team.

Stargate Atlantis
SGA is a spinoff of SG-1 in which humans take an expedition to Atlantis in the Pegasus galaxy, where they try to unravel the secrets of the Ancients. Their principal enemy is the Wraith, a hive-like alien species that feeds on humans.

In badfic
There are several possible varieties of Mary Sue in Atlantis. One is the (often teenage) female that is native to the Pegasus galaxy. She could be a runner like Ronon or a relative of Teyla.

The other option is a woman or girl sent from Earth to Atlantis. This also comes in two varieties: the girl in question has no one left on Earth to take care of her, but there is a relative on Atlantis. The unlikelihood of a child from Earth being sent to live on a top-secret base in another galaxy on the front line of a war is forgotten in the face of the Sue's powers, and there are many canon males, all at least twenty years her senior, for the Sue to fall in love with.

In the second variety this problem is at least tackled, as the Sue is giving a military rank. Often her rank is too high for her experience, or behaviour. These military!Sues often don't seem to know the first thing about the concept of following orders.

In badslash, Colonel Sheppard and Doctor McKay get it on. Repeatedly. Their canonical appreciation of women, and such minor difficulties as the impracticability of screwing up or down the chain of command and the DADT policy, are forgotten in favour of sexytimes. In mpreg, Sheppard is occasionally turned into a woman by Ancient machinery, but more often the Ancients inexplicably had machines to give men wombs in their rectums.