C.O.
Do hang in there. Hopefully, you thanked the other parent for contacting you. One thing I think is helpful for parenting this age is the concept of autonomy and responsibility.
In other words, you (the child) want more autonomy; you want to make you own decisions and plans, and be allowed to go places without parents, and even have the freedom to go or do things on your own. We want to you be able to have that - BUT it is our job as parents, always has been, to make sure you can handle the freedoms we give you. We didn't let you play outside unsupervised until we had seen that you would not eat rocks or sand or try to climb or do other dangerous things. We did not let you play in the front yard unsupervised until we could trust you to stay away from the road. When we saw that you were getting more responsible, we taught you how to safely go out in the road to get your ball. When we saw that you were responsible about crossing streets and staying out of traffic, and were beginning to make good decisions even when someone else chose to do something risky or wrong, then we let you walk to school or to the park or to a friends house by yourself, etc.
Bottom line, each time you show maturity and responsiblity (by good decisions, actions, etc.) we know we can trust you to be responsible with a little more autonomy. If you make bad choices or show that we cannot trust you in some way, then we know you are not able to handle that much responsibility for a while. It's not so much about punishment, but about our job as parents and how we make our decisions. IF you are ready for the autonomy/responsibility you want, then you must show it.
Hang in there. We've all made dumb mistakes, and we learn. As for the phone call, most of us have made a few prank calls. Since you were lucky enough to hear the call, you can decide whether the call was indeed just irresponsible mischief or whether the content or message (?intent?) was more serious. If you are worried about the content, say so. Tell your son what you found especially disturbing about it and why. Don't be afraid to confront him with how his actions may effect other people. ie - The girl may feel less safe in her own home or at school. Is that really what he wanted? More than likely, he already knows it was wrong and why. If he continues to deny that it happened or accept responsibility for his actions, then I guess I'd get more involved.
And last, but very important, check in with his teachers. Not to ask specifically about the phone call; but about how he is adjusting socially, about why his grades are not what you are used to, etc. Ask them what kinds of things are lowering his grades; do they think he doesn't understand, or is he not turning things in, or is he disruptive in class... It can be weeks, even months before a kids' records from other school arrive at the new school. They probably have no idea that the performance they are seeing from him might indicate a problem. And not knowing your son well yet, they won't notice a "change" in personality that could indicate serious problems either. But from hearing their observations, you will have a better idea whether he is just adjusting and testing, or whether something is very wrong.
It is possible that he is trying hard to fit in, and the most receptive classmates he has found at this school have been different types of kids than he usually hangs out with. At our house, we are big on "choosing what kind of person YOU want to be" and standing up for what you really believe is right (or even standing up for yourself "no, I just don't want to do that, let's do something else"). No excuses like "it was his idea"; you still choose your own actions. I tell my son (about that age) "I know you want to fit in, everybody does. But, before you try TOO hard to fit in, make sure you know what you are fitting into and that you really want to be a part of that".
Good luck. "Parenting is not for sissies."