What a terrible position you find yourself in. The needs of your children are conflicting, and both of them are very much in need of your help. There are things you can do.
First of all, you need to make sure your daughter is safe, that means that you'll have to set rules that they are not to be alone together at all. If you are not in the house, then you'll need to make sure that she is being cared for in a place seperate from her brother. At night, when you sleep, I would recommend that you put a lock on her door, you keep one key, she can have one.
Second, you need to talk with your daughter, letter he know that you will not be mad at her, and that if he, or anyone else ever touches her or does anything else that makes her feel frightened that she should tell you so that you can make sure she's okay.
Next, you need to get counseling for both children. They could go to the same counselor, but not together at the same time. Your daughter is going to have to work through what she's been through. Your son needs a chance to work through his own issues. He is still very much a little boy. He may just be exploring sexually, or he may be acting out because something has happened to him. A therapist could also help you work through the other behavior issues that he is having. If you can't afford therapy, there are many therapists who will work on a sliding scale, and there are also a lot of organizations that will help.
While you may need to change things for a little while to protect your daughter, try not to make your son feeling like there is something wrong with him, or that he is in some way "evil". That will just compound your problems. Treat it as a mistake that he made. If you treat him like he is bad, he'll live up to your expectations.
I hope that helps, if you have any further questions, please don't hesitate to hit reply.
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As far as the therapist goes, a good child therapist will be used to working with kids who aren't so sure they want to be there.
As for the discipline, the most effective method of discipline I've heard of for kids that age (and I used to teach 6th grade, so I know that age well) is as follows (it may seem harsh, but if you don't catch his attention now it will only get harder):
Step 1: Warning, explain to him that all of the things below are going to happen if he doesn't get his act together (be specific about exactly what he is doing that needs to change).
Step 2: (if the warning doesn't work, sometimes that is all that is necessary)
Remove EVERYTHING from his room and his belonging with the exception of the following:
- his bed
- a place to study if he has one (such as a desk or table)
- a light
- an alarm clock if he uses one, unless it has a radio
- a set of sheets
- one or two outfits, of your choosing
- school books and a book or so to entertain himself with
He loses all priviledges, he has no TV priviledges, he may not have anything in his room that you do not specifically approve of. He can not go out with friends or have friends in. He must come out and sit with the family for meals, and any other time you ask for his presence, otherwise, he is to remain in his room. The only person he can have in your room is yourself (your boyfriend would be okay too, if you are comfortable with that). He remains in this stage for 1 week, during which time he must prove that he is ready to regain a priviledge. If all goes well at the end of that week, he can have one item back (you can choose or you can agree together as to what that will be).
He gets that item back for the weekend. If you still feel that he is putting in his full effort at the end of the weekend, he is allowed to keep the item . If he slacks back off, it gets removed.
Step 3: He continues like this, regaining one priviledge a week. (you may decide after a set amount of time, perhaps a month, that he can have a group of priviledges back such as free roam of the house, friend priviledges, etc. If at anytime he reverts back to his old behavior he loses the most recent priviledges that were added and gets no new priviledges for two weeks. If it still continues, everything comes back out, and he has to re-earn his things back.
By the time he is back up to having all of his priviledges, behaving will be a habit. I've seen this work for kids whose parents and teachers were beginning to feel like it was hopeless.
Your welcome. Do give him the warning first though, sometimes just hearing it is enough to scare them to their senses. Essentially what you're doing is boot camp at home.