There’s a struggle between good and evil, and (I’m predicting) almost everyone in Sleepy Hollow falls on one side or the other.
The Horseman is “Death” of the Four Horsemen of the Apocalypse. The evil sect is assisting the Horseman and trying to bring forth the other three Horsemen in order to invoke the end of the world.
Crane’s wife is a “good witch” who cast a spell on Crane so he could survive in a kind of magical stasis, but Crane and the Horseman are linked by blood (literally; their blood mixed together when they were each “killed” on the battlefield) so when someone resurrected the Horseman, Crane was revived as well. She appears to be still alive but trapped in some sort of magical otherworld.
The rest of the series, I’m predicting, is going to be a lot of “who’s good and who’s evil,” lots of double-crossing and conspiracy, intermixed with a lot of flashbacks to the 18th century. Kind of a mix-up of elements from Supernatural, Grimm, and Charmed, with a dusting of The X-Files.