Charges out of nowhere??

Hello, My 19 year old son was involved with an incident back in July where he was driving his car on a military base in NY, and a 16 year old in the car decided to pull out an air soft pistol out(rubber bb's) and start shooting this thing out of the window of my sons car. My son told him to put the gun away, and he did so. The problem is, the 16 year old had struck a little girl in the back of the leg area(causing no medical damage at all). My sons car was pulled over about ten minutes later. The 16 year old confessed to being the shooter, and the Military Police forced my son to make a statement or he would be brought down the the station for an arrest(point being, this made my son nervous so he complied). My son made the statement, and he was told by more then one of the MPs that he was not goin to be charged with anything, and he was free to go.(So we thought!) Well, about one week ago( alomost three months later now!!) My son received a Certified later from the Post Commander, stating that he was now barred from post for 5 years. This would not be a big deal however my son works on post. Super long story short is, I guess I opened some kind of can of worms by going to the Commanders office, and requesting a conditional pass to allow him to continue working. While making this request we all noticed that in the MP police report it stated that my son had been charged three times the night of the incident. First degree assault, Second degree menacing, and some form of battery?? Also found that the next day the charges were reduced to Second degree assault, and menacing stayed as is. I have tried to obtain a police report from several locations on the Base, however all of them have informed myself and my wife that we are NOT intitled to any of the information that took place the night of the incident. Here is the real kicker. They have no record of any charges what so ever against my son( because they were never issued!!), and have no formal paper work stating that.(at this point its all being done verbally!!). I received a phone call from the JAG liason, and that person informed me that I need to now bring my son in to be RE-READ his rights (BS) and to now be charged due to the fact that they cannot find any paper work on him from that night. I was also informed by the JAG office that they more than agree that this was handled wrong from the get go, and they feel that it is VERY sloppy police work(they have since appoligized to us twice). Okay to wrap things up here, I received one last call from the JAGS office stating that they do not need him to come in at this point, that would like it if I came in and picked up the charges for him. I agreed and picked them up yest. I noticed that have once again reduced his charges. Now he has third degree assault, and the menacing is still second degree. Please keep in mind with this whole story here, that my son WAS NOT!! Charged with anything on the incident night. This is most likely a result of the parents of the little girl that got shot at being upset. (I don't blame them, I would be upset as well) Another thing that is tickin me off with all of this is, the 16 year old that did the shooting, was not charged with anything at all, and is now simply picking up garbage/cans for a period of 150 hours on the Base. He also lives 3 doors down from the little girl that got shot at on the M.Base!!!! You don't have to be a rocket scientist to figure out here, that something is very rotten with this whole scenario against my son. I am not saying that my son should be getting off extra easy with this case, but the charges are now going to create a criminal record for him, and that really stinks cause he has never been in any trouble AT ALL!! Not even a damn parking ticket in his life, and now all of this(Plus he has now lossed his job as well) Please toss me suggestions for out court date if you could, and please by all means let me know all of your feelings on what has taken place up to this point with my sons case. My thanks go out to anyone who offers some help.

Is there an investigator from the police department assigned to the case at this point? Is any further evidence being taken?