Note: for more fanfics, see the Fanfic forum on my discussion board.
Conquest: this story is a "big war" type of story which takes place in a timeline which diverges from the main Star Trek timeline sometime around the middle of the Dominion War. It is complete, and is also available as a PDF file.
Reign of Terror: this story is a much smaller and more personal affair than "Conquest", involving the Maquis. It is still being written, although you can read what has been completed to this point.