Softly Creeping by anonymous, ~1600 words.
Sympathetic and competent Jennifer. This one hurts. But the John & Jennifer interaction is great, and somehow comforting. (References to past sexual abuse, permanent departure of a major character.)
If you're a hardcore happy-ending McShepper, you may want to not read the fic this is a sequel to (you'll get the general gist of what happened in it from Softly Creeping), as the prequel is very bleak. (In case you do want to read it, the prequel is the silence of the stars and of the sea, ~2000 words, Rodney/John dubcon/noncon, no HEA.)
"The One with the Healing Cock" by anonymous, ~19,300 words.
Set soon after Jennifer arrives on Atlantis, this fic offers a take on the many facets of Jennifer, some of which we saw on the show, but all rather more interestingly done (and better integrated!) than by TPTB. There's hey-she's-young-but-unexpectedly-compete
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