Complex sentence: Both him and Bookman find that Lenalee's Innocence saved her life which has never happened before meanning hers is a "exception" they start to think that hers might be the "Heart".
Split into simpler sentences: Both him and Bookman find out that Lenalee's Innocence saved her life, which has never happened before, meanning hers is an "exception". They start to think that her Innocence might be the "Heart".