Cry Havoc by Ladyblahblah
This is one of my favorite Sterek fan fiction.
The Summary:
In Beacon Hills, the two-year war that’s been raging between werewolves and hunters has begun spilling over onto the civilian population. Meanwhile, in Boston, when the tattoo on Stiles Stilinski’s back is damaged on a late-night hunt he begins to have dreams that lead him across the country, drawn by an inexplicable conviction that he’s needed there. When he discovers that Derek Hale began the war after his mate was killed, Stiles finds himself being offered a strange deal: figure out how to bring the alpha's mate back, and peace talks can begin.
What is best about this book is how it takes established plot points and then expands it with new characters and new plots. The romance is slow (mostly as we see afterwards and flashbacks.
A must read.