Stargate Atlantis Season 2
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OverviewSeason 2 ran from July 15 2005 on America's SciFi channel - January 30, 2006 on Canada's The Movie Network, with the hiatus lasting until SciFi starting running season 3 in America on July 14, 2006. The show's focus for the season was on ethical choices episodes like "Trinity", "Michael", "Critical Mass", and the season finale, "Allies". Icarus observed
The idea that emerged in Season 2, that SGA metaphorically expresses America's militaristic attitude toward foreign policy, has been bolstered in later seasons with episodes like Season 5's "Inquisition", which fiercelydreamed described as"Some fans were frustrated with their un-heroic heroes, while others loved the moral complexity that echoed the growing cynicism and sliding support for America's Iraq war."
"a pretty sharp allegory to a certain kind of American self-interested, cowboy, interventionist, might-makes-right international political strategy that has seen some prominent use in the last 75 years." )
In fanfiction, that focus led to more stories about the military (such as Miss Porcupine's work), a growth in the number of stories exploring the effects of DADT on various slash pairings, and a more through examination of John Sheppard as a character.
"By 2006, slash fans began to take more of an interest in John. He became more important partially because of the complications of "don't ask, don't tell" on the popular McShep, as well as a natural need to flesh out both sides of the pairing. Unfortunately, unlike Rodney, fans discovered the reticent John gave little clear information beyond the fact that he likes Ferris wheels and doesn't apparently read Tolstoy. Until "Phantoms" in the fall of 2006, fans did not even know the real story behind John's black mark in Afghanistan." - Icarus
Despite the canonical focus on current events, SGA fandom still had a strong focus on escapist entertainment. Crackfic and AU continued to have strong audiences, with the Harlequin Challenge on sga_flashfic and reel_sga (for stories based on movies) making their debut. 
The episode Conversion caused discussion among Sheppard/Teyla shippers; some felt that the kiss undermined the credibility of John and Teyla as a couple, while others interpreted it as supporting evidence for their attraction .
Throughout the year, many minor characters were developed by various authors, including Lorne, Laura Cadman, and the new ships Lorne/Parrish and Beckett/Cadman. Possibly influenced by Cadman and McKay's genderplay in Duet, explorations of alternate sexuality also represented in a variety of different ways, including cross-dressing, genderfuck, and BDSM.
Several stories achieved high levels of discussion and controversy over the year as well.
Episode Reaction Fic Here
Duet: bodyswap stories; also Rodney bonding with Cadman
Trinity: pretext for much grovelfic/apologyfic.
Instinct/Conversion: John is a Bug with hella instincts.
- SGA thematic list: Wraith/Iratus bug transformations
- The Crate by rosemending
- Transition Point by Martha Wilson
- Shed Your Skin by seperis
- Theory of Evolution by Lavvyan
- Class: Insecta by cupidsbow
- Conversion Trilogy by margarks
Aurora: stories often exploit and explore the canonical virtual reality.
Epiphany: John deals with being abandoned
Grace Under Pressure: Rodney hallucinates Carter...or others. Tags also give comfort or distribute blame for the crash.
- Hydro-verse Trilogy by mk
- Grace After Pressure by Leesa Perrie
- Amazing Grace by cybersyd42
- How to Decompress by 30toseoul
- Graceful Exit by astolat
- Very, Very Improbable by Lacey McBain
- Beyond Oneiromancy: A Rationalist's Guide To Understanding Your Dreams by The Spike
Inferno: Norina brought us a rash of cockblocking stories
Minor Characters Here
The John/Rodney or "McShep" pairing continued to dominate the slash fandom, with approximately 70% of all slash fics uploaded to Wraithbait dedicated to John/Rodney.  There was an upsurge in interest for the Rodney/Carson pairing. Three new slash pairings appeared on the scene: John/Ronon, John/Lorne, and Lorne/Parrish.
Epics: McShep writers produced mammoth epics like Freedom's Just Another Word For Nothing Left To Lose and In the City of Seven Walls.
Crackfic: Crackfic continued to be popular; Arduinna's Candygram added whimsy to the team, in a story where John, Rodney, Ronon and a Wraith are turned into beanie babies, while skoosiepants's Once Upon a Furry Octopus series made the fandom collectively grin with its tale of a young furry octopus that steals Rodney's pens. In Human Enough , John is born a centaur. The B-Movie challenge helped increase the amount of crackfic, producing such works as The Roads Never Lead Where They're Supposed To Go by Eleveninches
Canon Universe Stories: Stories rooted in canon were still going strong, and stories like The Ratio of Burning by Stillane and Calligraphy by eretria proved popular. There was even a challenge for canon universe based stories (Back to Basics) in response to a feeling among many of the first-year writers that there were too many AUs being written.
DADT Stories: However, perhaps because the show also brought the characters back into contact with Earth, other slash stories began to take military regulations more seriously, or at least use them as a plot device. Stories such as amireal's Scenes From A Lesser War and Trinityofone's DADT, Damyata, Damyadvam were at least partly about the potentially serious consequences that slash romance could have for the characters. Some have argued that SGA slash writers still have more latitude than SG-1 slash writers because of the iconoclastic personalities of John and Rodney, the physical distance between Atlantis and Earth, and slashers' widespread belief Elizabeth would gladly cover for gay soldiers.
Multimedia Storytelling: Zoetrope's Missed The Saturday Dance was posted on October 16, 2006 and was immediately praised for its innovative use of multimedia enhanced storytelling; the story features both mp3 audio tracks as well as a trailer for the vid, while the story itself is largely composed of artifacts and images.
Crossgender/Genderfuck: You're Pretty Good Looking (For A Girl) by Trinityofone is a story that responded not only to the Season 2 Episode "Duet" by subverting our expectations of genderfuck: Rodney doesn't change back. This story is possibly the first "We're not straight, we just love each other" fic in SGA fandom. At the Violet Hour by Linaerys also delt with genderswap, by having John transformed into a girl.
Alternative sexualities: Toft Froggy posted Second Skin, a story she described as an "epic transvestite story" in May 2006. Xanthe's Coming Home, set in a BDSM universe, was also posted that year, leading to some controversy when Helen posted Take Clothes Off As Directed as a response to it in November 2006, describing the story as "an unauthorized homage". . The ensuing discussion, both about how fans felt about Xanthe's depiction of BDSM as well as community standards for rewrites/homages of other people's stories without author permission, and sometimes with active author denial, continued well into the following year. 
AUs: Fans continue to create popular AUs that have no connection to space or the city of Atlantis at all. Sheafrotherdon posts A Farm In Iowa (June 2006), in which John inherits a farm and Rodney stumbles into a life with him. High-school AU The Best Things in Life Are Free by Smitty was started in December of 2005, but it wasn't finished until February 2007.
Alternate Realities: Fans also produced alternate realities that featured Atlantis...but not. Stargate canon already gave fans the quantum mirror as well as multiple timelines, but with the episode "McKay and Mrs. Miller" (September 2006) we now had the Mensaverse. Many ARs were produced in the Mensaverse , and there were also radical reimaginings of canon in 2006 like Seperis's Crimes Against Humanity series, in which Atlantis is a penal colony and the cast were psychopathic criminal masterminds. Or Gaia 's Mau Loa Means the Time We Have, a story that was paced like a horror story, wherein John is living in Hawaii and runs into this old guy at a gay bar.
Horror: Season 2 really ramped up the horror aspect of both John&Rodney friendship stories as well as John/Rodney slash. For example, Sistinas By Jennghis Kahn had a still-living Sheppard playing a game of cat-and-mouse with Zombie!Rodney in a post-apocalyptic Atlantis.
General overview of Ships.
2006 also saw some of the most powerful gen stories in the fandom being produced. Freedom's Just Another Word For Nothing Left To Lose, commonly agreed the most popular story of the year, straddled the line between gen and slash and won a gen award although the author intended it as slash. Another story that connected gen and slash fandom was Samdonne's John Sheppard gen opus, Your Cowboy Days Are Over. It was a highly visible example of an ongoing trend that continued to move the fandom slowly away from its Rodney-centric focus. The story combined the complexity of ethical dilemmas that had no real right answers with a harder, more modern sci-fi basis and became a favorite for a lot of people because of its quality while others found it too depressing; a fate that it shared with Freedom.
In a complex examination of Runners, Domenika Marzione's Matter, Form and Privation explored the possibility of unethical Runners and the steps that Atlantis must take to deal with them. The author's stories tended to focus primarily on the military side of Atlantis with both knowledge and sympathy and tended toward a more military and military-eyed viewpoint of Pegasus. The Long Way Home by Friendshipper is a Texas-based AU that retells the stories of John, Teyla, and Rodney from a unique perspective. Scheherazade - In Wintertime deals with memory, identity with truly alien aliens and what makes a person who and what they are.
Ltlj continued her well-read series Retrograde, a complex gen novel exploring an Atlantis that has gone native and never connected again with Earth. While the first story, Retrograde, had been released late in 2005, the sequels, including the densely plotted Recovery, was a strongly John and team focused story.
- Stargate Atlantis Season 2 on Wikipedia
- Icarus' original article
- SGA 5x13, Inquisition.
- Icarus' original article
- reel_sga 
- Vabarella, Death of a 'Ship', 30 May 2006
- On October 30, 2008, ignoring the "bitextual", "threesome" and "crossover" categories etc, simply dividing the Mcshep/all slash stories numbers from their categories listing the number produces 72.5%
- Leah Human Enough on wraithbait
- Back to Basics community
- Comments, because it is very early and i'm very awake, September 23, 2006
- Seperis, midday, later than, September 20, 2006