Lyric discussion by Martinsherry16 

Cover art for Past The Mission lyrics by Tori Amos

I agree that the Mary Magdalyn/Christ interpretation makes a lot of sense, and a lot of posters have interpreted it well in that way. I've always seen it another way, however. The beauty of Tori's work is that it's often open to multiple interpretations.

Anyway, the melody always seemed spooky and sinister to me, so I always put a dark interpretation on the lyrics. My take is that the singer is a woman who had fallen into the clutches of a femme fatale ("she" and "hot girl" in the song). The first stanza describes the seduction. I picture the singer as somewhat innocent and inexperienced. A man has also fallen for the femme fatale, and she has killed him. She is definitely a psychopath, perhaps a serial killer (very unlikely in real life, of course, most serial killers are men). The singer strongly suspects the femme fatale is guilty of the murder. As for "the mission", I'm not sure about that; it could be where the man was buried by the murderess. Note that there's also a reference to prison, perhaps a foreshadowing of what's going to happen to one or both of the women. If you're the type who enjoys a sad ending, you could imagine that the crime has been discovered, and the singer has been framed by the seductress, and the former is awaiting her execution in prison, remembering the passionate relationship with her lover ("I smell the roses").

Or maybe I've just overdosed on film noir:)