But why would he be at any level of obedience since he was kicked out of his former school for being highly DISobedient? I mean, you don't have to be obedient in order to be held back by something. And I think that what's holding him back is a guilt and regret for his former actions, which is not the same kind of crippling effect others have. His grew out of his own actions. The others had them imposed upon them by society.
I do like the theory about the bears, though. I had had a similar thought some time ago but I didn't flesh it out nearly as well as you did.
I also wonder, now, similar to what someone else said, again, if John knew what the invisible attacker and the person with the bear were actually up to, if your theory about the bears is true, as well?
because his old school was not for high level tiers like this school, but they let John the school even from being disobedient. It seems like he may have made a promise with maybe his dad about how her can still do much even if the world thinks of him as a cripple. The dad did write the book at the time John got expelled. Claire seems to have used John for all that has been gathered. So that means power won't get him what he truly wanted a changed world so maybe his dad suggested that he try a different approach thus being crippled. you can see how things keep progressing because you see results from what sera just did, but I am not the writer so I can only guess until the puzzle becomes complete. I look forward to more chapters to see what happens. I also agree about that thought that John knew what the bears and invisible person were doing, but I don't think all of them are all on the right side maybe there are spies in the ranks as well, unless they wanted to make sure it was john plus provide a suitable distraction about the book for sera to use because that all seemed to flow too nicely if you ask me.
A couple things first, though:
1. Since his former school is for low tier students and the reason he was kicked out of that school was disobedience and that he's now at this school is to learn obedience, then I believe that says that to achieve the level of obedience from him that this school requires means he SHOULD have been started at a much LOWER grade than they currently have him at, especially given the implication your theory now has, that the expectations at his former school for obedience would also have been much lower for any student in general, and given that John wasn't even able to meet such lowered expectations. If however you mean that that school used disobedience as an excuse to kick him out then wouldn't his current school have realized it was an excuse since they would know all low tier schools have lower expectations for obedience and started him at a lower grade anyway? If you mean that low tier schools have NO expectations for obedience, then, again, high tier schools would know that already or at the very least there would be no recourse for the low tier school to punish him for disobedience in the first place;
So what I THINK is that John probably just missed one or two years of school. Given how traumatizing these past episodes most likely were and that this all seemed to have occurred much farther back than a single summer. I mean a low tier school keeping a shocking incident like that entirely to themselves seems highly unlikely unless the passage of time allowed even the smallest of rumors to run their course.
2. John was already at the very least acting like what is considered a conventional cripple in this world long before he met Claire. Unless you mean as the alternative definition of cripple that we were just discussing? But then why keep his abilities to himself at all?
However I do like your idea about there being spies within essentially a group of spies. And your theory about the suitable distraction does jive with my own theory about how smoothly that transition seemed to take place in my opinion too AND how this was subtly implied to be the case by the author themselves.

I think that everyone has it backwards for the bears. I think that Ember is the authorities, but that the people passing out the bears are trying to stop Ember, but they know the targets are uncontrollable higher-tiers so the group trying to change the government or peoples views are sending out the bears to figure out the moves of Ember as the saying goes to caught an enemy you must think like the enemy. I also don't think that John is as free as everyone thinks. John is suppose to be almost graduating high school, but is only has started back at the year he got into trouble. What if the school is trying to reform all the students before they leave and John has to start from there because that is the level of obedience he is at. These are just my opinion and it may take a few more chapters to find out if I am even close, but just have wait and see ┑( ̄Д  ̄)┍ so glad I only have to wait a week to see updates of this manga ヾ(☆▽☆)