If you were my best friend and called me/ said what you said in your original post, I would give it you straight, and offer the following:
Overall, there is some hope he isn't out yet but read
the policy- it presents that this now having multiple failures and after his prior mulligan, he very well likely will face a board. reality: He may or may not get another chance to pass the PRT. In the meantime he should do everything he can to maximize the opportunity
should he get one to retake the PRT (again). Balanced rest (to the extent possible in Bancroft), Nutrition, Stretching, remedial running club, Stan Smith's video's on how to improve your times, and IMO above all - unwaveringly consistent effort.
A friend of my DS in NROTC failed the PRT at least once a semester (most but not all failures in mock PRT events) but amazingly managed to squeak through and commission. A classic what do you call the person who graduates last from med school scenario (Doctor!) He finally after the 7th or so time got disgusted with himself, stopped the bouts of extreme or no exercise and terrible dieting) and now fitness is part of his daily life.
1. Whether or not your DS will have the option to continue to commission in another path, NROTC/ OCS etc. largely will depend on how he is coded out in his military discharge paperwork (DD214). He if that is necessary should discuss his desires.
2. He will have a transcript with each of his course completed from USNA. He should use the TCE transfer credit evaluation tool at each college he is interested in to get a very specific understanding of what will transfer there, and how those transfer credits will either satisfy specific or general education requirements toward a degree. It's free, just have to have a transcript and some course description documentation. That would help him know his options. He can also apply - many colleges still accept applications here in Feb and you can look up options, details. But I would direct energies to fixing the problem and staying for now, until he has more information.
3. See what veteran benefits he would be entitled to if separated. veteran benefits? Yes, he will get some - confirm which education benefits might be available (I have no idea).
4. Man in the mirror time - what is the malfunction and what can he do to fix it. He can't mentally muster a hustle to erase a 3 second deficit? Is he exercising consistently, overeating, is this a mental block? Does he want to commission and serve, still? is his heart in it, all-in? Or does he want out and this is his path. My DS would state those this close, it's perhaps a mental thing mixed with a lack of preparation/ consistency thing... or is it something else? find out, fix it. Your DS is training to be a leader and set an example - he needs to be above the minimum as an officer and these tests need to be a non-stress event. Why is he keeping himself near the lowest bar possible? Maybe an officer career isn't in the cards, or maybe like the example above he'll turn it around.
Recoupment: Find out if he will owe any moneys for the education received if he is separated, if he cannot make it to commission and serve. I have no data on this - go to the source.
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Good luck. As a fellow parent I have empathy for what your son and family are facing. If it would help you/ him to line up plans B, C, D and an improvement plan on the PRT readiness issue, I see no downside of doing so.