If Hermione still had any doubts of the existence of an entirely separate magical world, they were to be dispelled in a very nasty incident.
She had made no headway on teleportation, what Tom could do, no matter her efforts. Due to her competitive nature, she loathed that there was anything Tom could do that she couldn't. She simply refused to accept it; if there was something another person could do that was worthwhile she logically had to be capable of it as well. That was her motto and motivation in all her endeavours.
This time, it didn't pay off. Weeks and weeks of practicing and when she heard a crack and felt herself squeezed through a sightless tunnel, she emerged on the other side not in triumph, but in a world of pain and fear.
Tom heard the screams coming from Granger's home while playing (or practicing magic) in his treehouse and immediately knew something was wrong of a magical nature. He didn't need to ask himself how he knew, all his instincts prompted him to immediately teleport noisily to Hermione's front door as the screams (a woman) continued which were soon joined by the loud shouting of a man.
Tom used his magic to unlock the Granger's front door and rushed up the steps. He burst into Hermione's room, where the screams reverberated, and it was the first time he'd seen it… his first impression was that it was filled to the brim with stacks of books and papers.
Hermione was lying on the floor in a pool of blood and half her torso was missing. Her clothes were torn clean. She looked like she'd been mauled by a bear. She looked like she had died except for a few shallow breaths that were still rising from her prone body.
Overcoming the shock that coursed through him (and Hermione's parents as well who barely noticed him), he immediately began shattering every window in the Granger's home. If that wasn't enough, he levitated the bookshelves and Hermione's books were swept up in a whirlwind of his making with pages torn out, as they spiralled above his fingertips…
Mrs. Granger fainted dead away next to her daughter and Mr. Granger was dumbstruck and speechless.
Desperately, anything to raise the alarm through his "accidental" magic and it worked. Fifteen minutes later, Hermione was admitted into a magical hospital called St. Mungo's. Out of nowhere, wizards appeared out of thin air with a crack (which Tom noted was not dissimilar to the sound of what he could do) and after whipping out sticks (wands) they had apparently stabilised her and transported her to hospital. Tom went home after telling a terrified Mr. and Mrs. Granger everything he knew about the magical world, which was honestly not a lot.
Obviously, he had tried to keep his own role out of it but it hadn't worked. Hermione had blabbed. But he hadn't known the dangers that were involved. He had never experienced such troubles personally teleporting even longer distances.
It was only after a lengthy conversation with his "parents" who had presumably spoken with the Grangers that Tom realised how much trouble he was in. Hermione had severely splinched herself trying to "apparate" and if help hadn't arrived in time, she could have lost her life.
Obviously, he hadn't known the inherent dangers involved and to some extent he resented the punishment. Strangely though, he was not one hundred percent resentful. He recognised it was an oversight on his part to experiment with magic and the unknown which could have unforeseen consequences for others…
Tom felt... regret for the first time in his life. A smidgen of concern for her well-being if he was being honest with himself. If he hadn't goaded her on, in quite a deliberately manipulative way, she might not have pushed herself that hard. He hadn't expected this, of course but he grudgingly admitted it was a mistake to teach Hermione if magic was indeed so dangerous that he'd put her in danger. He was clearly not a good teacher namely because he didn't know what he was dealing with either and he hadn't been smart enough to realise this.
Tom was grounded for two weeks and not allowed out of the house except for school. Now the game was up with the Ministry intervening and all their parents were aware of magic.
"We aren't going to judge you on that," his "mother" said quickly.
"We cannot allow you to put yourself or others in danger before you learn how to control… your gift," his "father" offered with the appearance of being reasonable. "You've endangered a child…"
"She only spent a week recuperating at St. Mungo's," Tom pointed out, "quite amazing what magic can do to heal a person. It makes quite serious injuries in the non-magical world appear trivial."
His parents didn't know how to reply to that. What Tom resented the most was that Hermione had got to see the wizarding world up close. She had told him all about St. Mungo's and the wondrous things she had seen personally even as she was recuperating.
His parents had been allowed to visit. Probably in order to apologise on his behalf. Tom actually considered harming himself with magic, a non-life-threatening injury, just to be sent there so he could see for himself. His parents had grounded him causing him to miss their visit to Hermione and he would never forgive them for that.
So that meant no more secret meetings. No more magic at all until Hogwarts which would not happen for another two long years.
They weren't friends really and the accident seemed to have put a further strain in Tom and Hermione's relationship. All in all, Tom was simply exasperated with how rule-abiding she was even when it came to magic.
"They're your non-magical parents," Tom pointed out. "They don't understand anything about our gift, why on earth would you follow their advice on how to practice magic from your NON-magical parents?"
"We need wands, it's too dangerous," Hermione argued back in a rather formulaic fashion. "We don't know what we're dealing with and even the full-grown witches and wizards I spoke to warned against practicing underage magic."
But Tom never felt he needed a wand for his magic to work. He continued to secretly practice when his parents were not in the house. He wasn't going to be timid around magic (it was magic that brought him to another time after all) and he never had any problems. The more he tried, the more precisely he could do it until he managed accuracy within a step (even at nighttime without any light). The noise that he made gradually lessened until it was no longer a distinctive sound at all. He practiced so hard that even the light-headed feeling you normally felt upon completion of an apparition went away entirely.
"And anyways," Hermione said fidgeting which Tom could only interpret meant she wavering, "I don't want to disappoint my parents and you shouldn't either. They really have your best interests at heart."
Tom didn't believe that one bit and he felt exasperated that her solution for everything was just to "follow the rules".
"Muggles follow the rules, us magical folk we CREATE the rules and we can find ways past them thanks to our magic. That's what it means to be magical."
Hermione was not amused by this. Amusingly for Tom though, Hermione's dedication lasted all of two months. In the end, she had admitted at school that she had started using magic deliberately again, in secret.
"I suppose I just can't stop using magic entirely. I feel tormented if I don't do something every once in a while. I can't suppress it. But I only practice levitation which I've completely safely mastered at this point."
It wasn't much of a rebellion, but it was a start.
He had pretty much made up his mind that Hermione's muggle parents explained why she was less talented than him. It also explained why she was perhaps better able to fit in with the muggle world than he could. His real mother had never talked about his father but Tom assumed he had to be magical just like she was. He couldn't think of any reason why she would choose a muggle as her partner.
Another negative thing that came from all this was that Tom sometimes felt like he was being watched. He wasn't sure if he was being a bit paranoid but every once in a while he could just sense that someone (probably magical) was tailing him, even around the house. Of course, no matter how angry he got in response, he could make neither heads nor tails about this mysterious person and it made Tom feel more powerless that he resorted to practicing his magic even harder.