The last book (spoilers)
So i finished it. So apparently back when the girls were going to steal Ali's flag back in the 6th grade her twin sister Courtney was home from a mental hospital. Courtney stole Ali's ring that said A on it and convinced her parents that she was Alison instead of Courtney so Ali went to the mental hospital instead. So Courtney did all that horrible stuff while Ali was in the hospital. So on the night "Ali" went missing Ali killed Courtney. So Ali was A after Mona died and somehow got the diary where Courtney (posing as Ali) wrote all those secrets.
I think i got that right. Wow