While students do withdraw from private school for many reasons, they do not normally do so weeks before the end of junior year, and the failure to provide an explanation for why he did so is likely to be problematic. He wasn’t failing, the family didn’t move, and the tuition would have already been paid, so the probable reasons remaining are limited. If there is a good story to tell, students are generally encouraged to be upfront about addressing the issue in the application, or by a counselor letter, hopefully showing that the student has overcome the reason for the withdrawl. Colleges may be understandably concerned about unaddressed mental illness which may be continuing, or other unnamed reasons for withdrawl. I would ask a consultant how to best handle this issue now and on the common app, if he is using it.
Thank you for all your responses! It has been extremely helpful. I feel better about the situation. We are going to contact a college counselor to discuss my S’s option. He is changing his focus to less intense/less competitive colleges now that he knows he isn’t comfortable in those situations. I agree with many that leaving with a few weeks left in the year raises a red flag. He realizes that the consequences he is now facing is a result of a poor decision to cheat but is willing to work extra hard to prove it was a one time event. I’m glad I found this website.
Thanks for thinking of me, everyone. I think a lot depends on what kinds of colleges he wants to apply to. If we’re talking about large and not terribly selective schools, they may not be all that sensitive to red flags; they see the numbers they need and they admit. If you’re looking at schools that are smaller and/or more selective, I’d probably level with them about this, and it could be beneficial to get some help writing that explanation.
I’m wondering how and from whom he will get credit for the second semester of classes?
The advice to apply early to rolling admissions schools seems like a good idea to me. If the results are not favorable, perhaps contemplating a gap year, enabling him to submit a full year of grades at his new school might help?
Hanna is the expert, though. 
ETA: happy to hear that your S is springing back. It will all work out for him in the end.
I’m glad Hanna weighed in. My opinion was going to be pretty much what she said – that it’s really going to depend on where your son applies. Do you know what your in-state public options are like? Would your son be interested in going there, and does he have a good shot at them? If not, or if your son really wants a small private school, the situation changes.
However, if I heard that a student had switched schools late in junior year, I would not at all automatically assume that the student was expelled. Maybe there was bullying or the student had other social problems that made that school simply unbearable for them. A caring parent would not force such a student to last out the end of junior year, especially if the student’s anxiety or depression might affect their grades.
So I would suggest saying something on his applications like “in spring semester of junior year, due to my growing stress and anxiety about continuing on at School A, I made the decision to transfer to School B in March. My mental health improved immediately and I have loved my School B experience, including having the opportunity to [maybe mention one or two things about his senior year – being on sports teams or in clubs, taking a class he really enjoys, etc.].”
I’m pondering whether ethics and honesty requires him to come clean about the cheating. My feeling is that, since the school has stated they will not disclose the incident, and he has undergone the disciplinary action they gave him (2 days’ suspension and withdrawal from the class), he is not required to disclose it himself. Obviously he shouldn’t lie if questioned, but that’s different from affirmatively telling the story right off the bat.
Every high school gets to make their own decisions about what the consequences for cheating should be. Your son is not required to add additional consequences on to what the school has decreed.
Make sure that you submitted the latest report card from the private school to the high school. The school will probably use these grades in combination with the grades at the current high school. One challenge is that your son may not have enough seat time at the public school to get credit (you should definitely discuss this with the guidance counselor to find out how the high school handles this). Some high schools like colleges, do not transfer grades only credits. You will need copies of his transcript from his old high school, which will be sent to colleges along with transcripts from his current school.
Agree to seek some assistance in dealing with this on his applications. Most schools will ask:
Common App Question: Have you ever been found responsible for a disciplinary violation at any educational institution you have attended from the 9th grade (or the international equivalent) forward, whether related to academic misconduct or behavioral misconduct, that resulted in a disciplinary action? These actions could include, but are not limited
to: probation, suspension, removal, dismissal, or expulsion from the institution.
If he was suspended for two days the answer to that question will be yes and he will have to explain what happened,
As a parent, I would be less concerned with college right now and more concerned with my son’s moral development and mental health. I happen to know that cheating is fairly rampant among young people and resisting that culture in some schools takes real strength. So I am not getting on a high horse here at all.
I understand he was suffering and this is not useful at this point, but I think that the discomfort he felt might have been a helpful consequence in some ways. Is it possible he might have learned he could overcome that over the next two months and re-earn respect? I don’t have a sense of timing but it seems as if he might have benefited from finishing out the year, in more ways than one. Obviously for transcript, but perhaps for learning how to handle things in the future.
I think he should come completely clean with colleges about this. And say what he learned from it. Some will ask anyway. But it is better for him, personally, to face up to this rather than cover it up and try to flee from all consequences.
I think the approach of a parent should be to help him forgive himself. You really cannot run away from yourself: you wake up with the same ten toes as my father used to say. He made a mistake and many will understand. It is a heavy load to move forward trying to cover it up.