Well, personally, what I would do depends on whether the child has yet hit the puberty growth spurt. If not, some sixth grade boys are still smaller and not much stronger than their mothers, in which case I would quite simply take him to school. Put him into the car (I've done it with a 5th grader, so sixth grade might or might not be extremely different), engage the child locks, drive to school, park and commence getting him into the building.
I'd tell him he has a choice of how he arrives, but not a choice of whether he does. He can either walk in (and I'll be emailing his first period teacher to make sure he arrives where he's meant to be) or I can take him into the building -- whether that's simply grabbing him by the arm and walking him in, or whether he resists so much that it requires me carrying him into middle school like a stubborn sack of potatoes just the way I put him into the car.
Here's more of how I'd discuss this with my kid in similar circumstances:
He's had a lot to deal with in his life, and none of that was appropriate or fair. Yes, this absolutely sucks. But acting out will not fix it, and attempting school refusal is hurting nobody but himself.
If the legal system hasn't provided satisfactory avenues for solving the issue, he and Mom need to just be their own team to get him the best life possible... on Mom's part, that means saving aggressively so that she can afford for him to either move in full time with her (no child support) the day he turns 18 AND pay for at least community college, or to set him up in his own apartment near any college he gets into that he can afford between scholarships he earns & Mom's contributions.
He can leave and never look back the day he turns 18, but only if he's done the work up to that point to set himself up for a promising future. Mom will guide him and help him as much as he can, but he needs to do his part to responsibly shape his desired future. At his age, that's getting the best education he can and using that as his eventual ticket to independence.
Furthermore, the other parental figures in his life may be completely failing him, but Mom is determined not to. She'll fight for him & do right by him in every choice that's hers to make. One of those such situations is refusing to let him become a troublemaker, or a kid with a bad reputation, or a kid whose poor choices have already made his future harder.
School is not optional. Firstly, it's the best thing he can do for himself. Secondly, it's a parent's responsibility to see to it that their kids get good educations.
I'd ask what about school was objectionable, and I'd tell him that I was 100% committed to working with him until a solution acceptable to him, to me, and to applicable other parties legally required to have their input considered. We will try to fix things. I'd promise (and keep my word!) to check in with him frequently and not stop pursuing adjustments/improvements to his school plan until he agrees that it feels acceptable to him. BUT I would also tell him quite frankly that it would likely be a long process, and that while I would keep at the issue until a satisfactory resolution was achieved, his part in all of this was to continue going to school and doing his absolute best at his schoolwork while I worked on a longer term solution. I would promise him weekly progress reports, and require from him/his teachers weekly attendance/behavior/effort/grade reports, and that would be that.
I am unquestionably on my children's side to work through any problems they may be experiencing, but that doesn't mean it would ever be acceptable for them to make shortsighted choices that hurt no one but themselves (school refusal, lack of the strongest possible educational background). In fact, in my view, if I let such a thing be an option I would be completely failing my kid. Kids can't always be the strong ones who do the right things; sometimes they need adults to take choices they can't handle out of their hands, and simply tell them what they're expected to do while the adult works on the big picture issue that was overwhelming them.
People will probably say I'm too harsh or that the child needs a gentler approach that's mindful of his traumatic past. Alright, maybe. I don't claim to be an expert, and obviously no one is obligated to take advice from an anonymous stranger online. One thing I will say, though, is that I had a pretty rocky childhood with some things that would definitely fall under most definitions of trauma... and I figured out right around this kid's age that in my case no one but me would care or help me, and that getting myself off to college was the only way to break out. Kids are tough, especially ones who have been toughened up by life. This one is being a little punk and acting out, sure, but I think when someone sits him down and gives him (1) the truth of his situation -- his behavior is not going to do him any favors -- and (2) a frank discussion of what concrete steps different people are responsible for doing in order to help him progress towards a better situation, he'll likely rise to the occasion. Sometimes the only way out of a messed up situation is to keep your head down, focus on the only things you can control that'll eventually get you some control over your own life, and fight until you break through at the end of a long, grueling effort. Sometimes there are no good answers or soft solutions. Sometimes tough truths and hard fights are all that's available.