This is set 10-15 years postgame of gen 4/5, and does not take into account BW2 at all. It's dark and includes major character death, serious violence, transphobia, negotiated non-monogamy, and some of the stories have other warnings listed as well.
Roaring Snow as Sand: a remix of kistuneasika's Moments Through An Hourglass, which is also assimiliated into my comaverse headcanon (and is seriously amazing, I'm biased because it was written for me but it is like the best thing, you could read it instead of my fic, that would be fine). Moments is Silver's story, while Roaring is Kotone's. The later two works contain all of the plot details you need to understand them, but this fleshes out some additional things. ~8K words.
New Game +: pokebb 2011 work, in which Team Rocket and Team Plasma team up and threaten to conquer all of the regions using cloning technology. Focus is on Silver, with some Green, Kotone, Cynthia, and N/Julie. ~17K words.
Collections of Elegant Formulas: pokebb 2012 work, completes the main plot arc, focuses on Silver, Black, N/Julie, Iris with a bunch of other characters thrown in. ~19K words.
No Specific Series/Universe:
Feeling Words: Kotone/Silver, a pinch hit for a holiday exchange. It's nice to write them with less trauma. PG.
Seeking Evolution: Leaf grows into Fire, Red grows into a Champion, Green grows into kindness, and a Pokemon tells a dirty joke. Trans themes, a little bit of exploration of inter-legendary dynamics, and the ever-present Red/Green. NC-17, though just barely.
Six Short Sketches: I like these although if this is the only thing of mine you read you would sort of think I am a misandrist :/ A variety of characters, stalking, workplace sexual harassment. (Why did I think the universe needed Pokémon workplace sexual harasssment fic?) Mostly Gen II and V characters, also Cynthia.
Sinnoh Liepard: this is human/pokemon porn, played mostly for laughs, except I accidentally put in a plot. Cynthia/Houndoom, Cynthia/Fennel, broken Juniper/Fennel.
Queen's Gambit, Accepted: an attempt at doing something over-clever with a game of chess. I don't think it quite came together, but hopefully interesting if you speak fluent chess, or really want to see Silver, Kotone, and N/Julie in a weird poly something.
Sing Yourself Back Together: my first piece of fic ever, written for megageek for the 2010 Holiday Exchange; Flint/Volkner Poké-Karaoke fluff with bonus Dawn and Kotone.
In which Scourge Sisters aren't very good at negotiation, and Seers perhaps are: Femslashex 2013 pinch-hit because I felt like writing 3200 words of pesterlogs in one evening apparently? Vriska?Terezi and Rose<>Terezi.
HSWC bonus round fill pesterlogs: Eridan<>Feferi to Mother Mother, John/Vriska friendzone with bonus Dave, Karkatc3<Tavros/Equius