Your story has a great many plot points that i like - independent harry who is powerful and stands up to dumbledore and his friends when necessary. Harry is interested in learning and is willing to use his fame for good if necessary.
However, you may have overdone the independent and the powerful part. I get that harry is powerful but giving him the power to make someone a squib is a bit much. Harry has studied magic from the same books as everyone else and used the spell to understand better. I get it that he can pass his newts and everything but even voldemort and dumbledore who have studied magic for far longer than him(even considering his spell) are not as skilled.
Next is the part about him hitting malfoy in a previous chapter. That was hypocritical. He had just had snpape arrested for only pulling a wand on him when he had started the whole thing by insulting snape in front of the great hall but that is ok, understandable even because snape always bullied harry. But with Malfoy the enemity went both ways. Harry has a lot of power, he could just have incapacitated malfoy and gave him a sample of his power instead of beating him within an inch of his life- taht is similar to what voldemort does to enemies who he has within his power. Harry after all is far more powerful or skilled than malfoy who was subdues and no threat to harry. And the approval by mcgonagall of his behaviour is ridiculous- the only way to deal with bullies indeed - then you must approve of what riddle did, he after all only hurt his seniors in the orphanage. Power used with restraint is justice otherwise it is mindless violence. A better way to deal with malfoy would be to incapacitate him and show him that harry a half blood had defeated three purebloods without even using his wand. That ought to have been sufficient warning and next time you caould have escalated a bit.
I don't approve of what pansy was doing but the punishment was a bit much. A few days without magic would have been enough to teach her a lesson, on repeat well the you could have gone ahead and made her a squib- though i still believe that giving harry that much power so easily is overkill.
Next is this chapter. Harry is resistant to intimidation and is powerful, we get that. NO need to rub it in but you are doing just that. Mcgonagall is responsible for the students of the school, and for two students to be missing for a long time especially when one of them is wanted by the board and her own positino is in jeopardy. I believe she has a legitimate right to be angry. Harry as an adult has full rights to leave the castle but he must inform the headmistress that he is leaving if not the destination especially as he is taking another underage student with him.Instead we have harry doing what he hates, intimidating mcgonagall with his power. You may argue that he didn't use it on her but to show the headmistress that she can't do anything to you even tough you may be in the wrong, i believe i would call that intimidation don't you? Harry's indiscriminate use of his power(remember snape) on the two occasions with mcgonagall and snape makes him a hypocrite. He could simply have told her that he was out and apologiseed for not informing her, after all mcgonagall has helped him. He must at least try to understand her position. His wanting to perform everything by intimidation is not really positive considering he now prides himself on his critical thinking skills. For all that he wants people to stand up for themselves it seems that is only limited to when they don't stand against him.
I think you must take a look at just what harry is becoming. Standing up for yourself is all well and good but a big part of being an adult - which harry claims to be is acknowledging one's mistake which harry fails to do.
Author's response
First, let me thank you for taking the time to review in such detail.
Overdone? I disagree. I have made it clear, from the very first chapter, that Harry is able to see, sense, and manipulate magic in an extremely unusual way. His studies are not what give him more power; several parts of the story show that the power is not within him, and that this is something nobody else has. "The power he knows not," in this case, is Harry's ability to see and natively control magic without spells using only his mind, which is the reason for the title of the story. The studying is just to help him get the "mind" organized.
Malfoy and Pansy are both bullies of the worst sort. Harry's reaction is not to any single action of theirs, but to the fact that both have been bullies and thugs all their lives. You may disagree with how I think life-long bullies should be dealt with, but that is explained in the story too.
McG did NOT approve of what Harry did to Malfoy. This is clear, and explicitly explained, in her internal conflict about what she should do about it at their fist meeting after that event.
Later, yes: McG has a legitimate right to be angry. That is not what Harry is reacting to. I'd suggest reading it again; her reaction to his departure is not because he departed, but because she is upset about something else being held over her head, and she's taking it out on him because of her own frustration. Harry recognizes this and refuses to wear it.
So, "Power used with restraint is justice"? Who said anything about justice? Harry is eliminating perceived problems and sending public messages. But if you don't agree, that's okay; you don't have to.
Lastly, one should only acknowledge a mistake when one is mistaken. On Harry's very first day back at school, he informed McG that he wouldn't be sleeping in the castle.
Thanks again for your review, and thanks for reading!