Not Quite Dark Magic by hiccupfound -- Chapters 24-31 (end)

Five years into to the war, the Order is pulling ahead after ages of drastically losing. Draco Malfoy notices. He wants in. He offers himself as a double agent, but the Order requests more. They've created a new spell that binds two people's magical cores together in order to make a nearly unbeatable pair of duelists. 

Draco agrees to bind himself to the person most compatible with his magical core. Even if it is Hermione Granger.