Shadows Of The Heart
Shadows Of The Heart is a story written by Haitoku no Honoo and illustrated by Jeromu Furijito. It ran in Issue 22 at http://s2b2.livejournal.com/122722.html, and is mirrored at http://www.shousetsubangbang.com/mirror/shadows-of-the-heart/.
From pinboard.in: "The one about the spy with a talent for walking through shadows and the pirate captain (who is actually a captain in the enemy forces) and their love"
From delicious.com: "Dave gets rescued by a pirate ship and discovers that the Captain, Ian, has a secret that will effect Almenia's war with Rhyanda. Fortunately he has his own secrets. Great story."