Each chapter is a TAG; each is complete and can be read stand alone although as in the episodes, there are continuing themes.
Pairings: Having rewatched the entire series, my view is that the show suggested multiple probabilities in regards to UST pairings (e.g. John/Teyla, John/Elizabeth, John/Rodney, Teyla/Ronon, Elizabeth/Caldwell, etc.) which I'm likely to explore (some more than others) alongside the actual canon RST pairings (e.g. Elizabeth/Simon, Teyla/Kanaan, Rodney/Katie, Carson/Laura, Rodney/Jennifer, Ronon/Jennifer, Ronon/Amelia, etc). There is an author's note preceding each story with any specific dynamics highlighted for those who like to be forewarned.
The index is organised by Season. The episode title is first with the TAG title following. If the TAG is blank, it means it isn't written yet. :)
Rising: Changed Circumstances
Hide and Seek: Ready or Not
Poisoning the Well:
The Storm/The Eye:
The Defiant One:
Before I Sleep:
Letters from Pegasus:
The Siege I & II: see Season Two
The Siege I, II & III: