Harry had insisted that he couldn't explain to Hermione why she was growing, at least not until she learned occlumency. This was because he couldn't risk a skilled legilimens learning the details surrounding her resurrection and the rituals Voldemort had performed. He couldn't even tell Hermione why he couldn't tell her, yet.
Understandably miffed, Hermione reluctantly agreed to wait for her answers. She would certainly not become a proficient occlumens before the start of term, however, given everything else that was happening that summer. She only insisted that when Harry did ultimately divulge his secrets, his reasons would retrospectively stand up to her scrutiny.
It turned out that when Hermione used her patronus to destroy the dementors at Azkaban, she'd unintentionally blinded the guards stationed there. When that came to light (no pun intended), Harry covertly arranged for the Stone to be used to cure their blindness.
With no lasting damage to the guards, the Wizengamot was divided as to what they should do with the girl. As it turns out, murdering a dementor didn't technically constitute a punishable offence, since until very recently, it was thought to be impossible (and on top of that, dementors weren't legally classified as fully-sentient beings with all the rights of a Wizard anyway, and they weren't paid, so they couldn't even qualify as Ministry employees or contractors), so the only thing she could be charged with was endangerment to a magical species population... that wasn't technically considered endangered.
The presence of her new phoenix familiar at the trial, however, ultimately swayed the jury to let her go with a token 100-galleon fine, which was immediately paid for by an anonymous benefactor. Hermione had her suspicions as to her benefactor's identity, but didn't question Harry about it, instead only giving him a kiss on the cheek when she was finally alone with him once more.
Hermione's rapid growth continued through the summer, but she'd been careful to stay secluded in Harry's tower throughout (making exceptional trips to the library), so only Harry and some of the school's staff were aware of her current predicament.
By the end of August, Hermione stood seven feet tall in bare feet (she gave up charming her shoes to grow with her, since with her limited skill level, the complicated charm required periodic refreshing, and she found her troll-enhanced physiology rendered her immune to stubbed toes and her skin immune to being cut by stepping on sharp objects, and her regenerative power kept the soles of her feet perfectly soft and callus-free anyway; in fact, combined with her toenails always appearing immaculately pearlescent (as a side-effect of the ritual with the unicorn), and her skin having a permanently-super-healthy and slightly-translucent glow, she had the most perfect human feet on the planet and could be a foot model if she had the inclination for such an un-ambitious career). As her body seemed to maintain her original proportions as she grew for some reason, the length of her feet remained one-seventh of her height, making them a true foot long.
Harry had to enlarge Hermione's bed and desk (using the Stone to make the size changes lasting). He'd gotten McGonagall to make all the doors in his tower taller, so Hermione wouldn't have to duck through them. The process would have to be repeated for the doors to all of Hermione's classrooms once the term started.
Two days before the welcome feast, Harry went to Hermione's room to talk. He had developed a special knock for her, involving tapping out the prime factors of the current "knock number". She would reply by tapping out the lowest composite number greater than the current knock number, which would be used for the next time. It was entirely too geeky.
Hermione opened the door, admitting Harry into her current home, and moved to sit on an enlarged sofa. Harry joined her.
"How are you doing?", he asked.
"I'm...admittedly a bit anxious. About all the students seeing me like this, I mean. On one hand, I'll make a really easy target for their teasing. On the other hand, I can't let anyone bully me without responding appropriately, since I'm trying to be a role-model..."
I've been thinking about that myself," Harry admitted. "Actually, I have a...proposal...for something that might help."
"Oh? Does this plan involve shrinking me to normal size before breakfast each day?", Hermione questioned. "Magic used on me isn't as effective as it used to be before I was resurrected as the princess with unicorn innocence and troll-like regeneration..."
"No, I wasn't proposing to shrink you," Harry began to explain. "Actually, this has several relevant factors, so please hear me out before you begin protesting, ok?"
Hermione arched an eyebrow. "Alright, I'm listening..."
"I mentioned the vow Voldemort put me under, which severely restricts where I can go. For the forseeable future, I have to remain on Hogwarts grounds..."
Hermione nodded for him to continue.
"This will have a negative impact on my mental health, and will largely limit my ... potential future spouses ... to those who also either teach or reside at the castle..." He was starting to blush.
Hermione cutely bit her lip, knowing that that very same vow meant she'd probably be working closely with Harry and also living in the castle for the forseeable future.
"I expect you're going to feel isolated from most of the other students, if not because of your height or "unicorn princess" status, then because you and I will be spending a lot of time alone making plans and conducting experiments..."
"...Go on," Hermione said encouragingly.
"We're both at an age where we need some sense of normalcy and security, and the more you grow, the more difficult it'll be for us to interact in any normal way..."
"Harry, what are you getting at?", Hermione asked, reaching for his wrist on the couch cushion beside her.
"I'm getting to that, I promise," Harry said. "There's also the lack of clout I have with people who discount me because they see me as just a kid...so this is where the idea sounds silly," he warned. "I want to use the Stone for...essentially a cosmetic purpose...to enlarge myself in increments to roughly keep pace with your height." He paused here, biting his lip while canting his head up to gauge her reaction.
"So between the two of us, we'd be about the same height, and do all our research work and relaxing together in the tower, modified to suit our proportions, and...you'd be my giant boyfriend who would beat up anyone who said something untoward about me? And if anyone questions us why we're giants, what will you tell them?", Hermione asked.
"I'd just tell them that it's nothing we're at liberty to explain."
"Won't this be horribly inconvenient for you though?", Hermione asked, tuning on the sofa to face Harry, tucking one foot under the thigh of her other leg.
"Not really, since I may be spending the rest of my life in the castle anyway. There's not much that I'd have to adjust here, really, beyond our tower."
"And if things don't work out between us...?", Hermione questioned.
"I could always return to roughly whatever my normal size would have been," Harry answered. "The Stone will remain under my control, after all. It just comes down to...whether you'd be comforable with me being the same size as you."
Hermione looked like she was holding back tears. "You'd do that for me?"
Harry beamed a smile back up to his 'girlfriend'. "We could arrange it tomorrow... then when the other students arrive for the feast, not all pairs of eyes will be staring at you, only half of them," he joked.
Hermione leaned forward, and held Harry in a long embrace. "Thank you, Harry. I'd like to try this. But what will you tell the professors? And the Wizengamot if they inquire about it?"
Harry grinned. "Just leave that to me."
