You and your son should speak to an experienced educational attorney regarding the possible school expulsion, and an experienced juvenile criminal law attorney. If your family cannot such attorneys, you may be able to ask the school district to refer you to an advocate for the disciplinary proceeding, and your son may ask for a public defender to be appointed when you get to court.
If your son refused to consent to a search, he may indeed have been in the wrong. California and federal courts have granted school officials very wide (but not absolute) authority to search students and their property. Children are generally required in California to obey all reasonable directions from school personnel. Only an experienced local education attorney or pupil advocate will be able to advise you and your son, based on the specifics of the case, whether or not he has a defense to either the juvenile court petition, or to the expulsion proceedings, and effectively prepare your son's defense.
Your son needs to speak to a juvenile criminal defense attorney ASAP. It is very difficult to determine what advice or direction to give you based on what you have written and he would be better served by sitting down with an attorney who can listen to more of the situation before advising him.
He should not speak to anyone from law enforcement before speaking with an attorney.
Ms. Cox has the situation "nailed" Peraps you shoul give her a call?
The above is not intended as legal advice. The response does not constitute the creation of an attorney client relationship as this forum does not provide for a confidential communication.