Are you thinking of the Out of the Darkness stories by Lexi Krycek?
Part 1: http://ditb.org/terma/ratbfic/lexikrycek_outofthedarkness.txt
Part 2: http://ditb.org/terma/ratbfic/lexikrycek_outofdarkness2.txt
Part 3: http://ditb.org/terma/ratbfic/lexikrycek_darknessjournals.txt
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