This was an email I recieved from a group I'm in. I absolutely love the points in this email so I'll share them with you

"Hi everybody, Reasons why Harry and Hermione will be together

Saint Seiya

H/Hr rule


Hermione is very thrilled when she thinks it's both she and Harry who will be prefects this year - she "just knew" they would both be prefects.
(The Woes of Mrs. Weasley.)
Additional Note: Hermione became quite flustered when she learned it was Ron who made it as prefect. It's my opinion that she was disappointed.

After telling Hermione that his scar hurt during his first detention with Umbridge, Harry decides to go to bed and a relieved Hermione decides that would be a polite way for her to leave the common room too; she excitedly invites him to help her knit hats for the house-elves. Harry tries to look tempted to accept the offer but still declines, leaving Hermione looking disappointed.
(Detention with Dolores)

When Harry returned from another detention with Umbridge, he was pleased to see that Ron and Hermione were waiting for him in the common room especially as Hermione, (Harry noted), was more disposed to be sympathetic rather than critical.
(The Hogwarts High Inquisitor)

It was Hermione who gave Harry a bowl of pickled Murtlap tentacles which eased the pain on his hand after he went to detention with Umbridge. It wasn't stated whether she got that from the hospital wing or she made that herself. Either way, it showed she was concerned about Harry enough to produce it.
(The Hogwarts High Inquisitor)

Hermione and Ron try to convince Harry to teach them Defense Against the Dark Arts, while Harry angrily tells them they really don't know what fighting the Dark, or Voldemort, is like. Hermione quietly tells him that that's exactly why they need Harry to be the one, because he knows "what it's r-really like... facing V- Voldemort." It's the first time she ever says Voldemort's name, and more than anything else, it's this that calms Harry.
(The Hogwarts High Inquisitor)

Here's Proof #2 that Hermione's almost always in Harry's mind or is part of his mind.
Quote from Book:
"For a moment Harry was tempted to go with Dobby. He was halfway out of his seat, intending to hurry upstairs for his Invisibility Cloak when, not for the first time, a voice very much like Hermione's whispered in his ear: reckless. It was, after all, very late, he was exhausted, and had Snape's essay to finish."
(Dumbledore's Army)

Harry comes back to the common room late after he and Cho kiss. Hermione briskly asks if they kissed, frowning. When Ron asks if Harry's a bad kisser and that's why Cho cried during it, Hermione (engrossed in a letter to Viktor) absently replies that of course he's not. Hermione overall is emotionally stiff, then later distant, in this scene.
(The Eye of the Snake)
Additional Note: I found it funny that Hermione would retort that Harry's "not a bad kisser". Has she been hopin' he isn't? Hehe....just a thought.

Here's Proof #3 that Hermione's almost always in Harry's mind or is part of his mind.
Quote from book:
"Harry dreamed he was back in the DA room. Cho was accusing him of luring her there under false pretences; she said he had promised her a hundred and fifty Chocolate Frog Cards if she showed up. Harry protested . . . Cho shouted, 'Cedric gave me loads of Chocolate Frog Cards, look!' And she pulled out fistfuls of Cards from inside her robes and threw them into the air. Then she turned into Hermione, who said, 'You did promise her, you know, Harry . . . I think you'd better give her something else instead . . . how about your Firebolt?' And Harry was protesting that he could not give Cho his Firebolt, because Umbridge had it, and anyway the whole thing was ridiculous, he'd only come to the DA room to put up some Christmas baubles shaped like Dobby's head . . ."
Hmmm...Cho and Hermione both appeared in Harry's dream. Cho turned into Hermione. A sign of a future transition perhaps? With Cho being a big whiner and Hermione being calm(in the dream)...who'd you prefer?
(The Eye of the Snake)

Christmas at Grimmauld Place. Harry was pretty much convinced that he was possessed by Voldemort and that the others don't want to have anything to do with him. He avoids contact with the others and hides in Mrs. Black's room, not planning to come out even if he's stomach was growling with hunger. Hermione unexpectedly shows up (having cut her vacation short to come to London), demanding to talk to him. Harry opens the door without protest and who else is in the room other than Harry and Hermione? Buckbeak the Hippogriff of course! Interesting how JKR puts this symbol of love where our couple is. Plus, Harry follows Hermione without any arguements.
(Christmas on the Closed Ward)

Hermione's reaction to Harry and Ron's Christmas presents: she's really happy with Harry's present to her [a book she'd been wanting for ages], and not so enthusiastic with Ron's [a bottle of "unusual" perfume].
(Christmas on the Closed Ward) - sent in by Sarah

After Harry's disaster of a date with Cho, he confides to Hermione what happened. Hermione, with strange patience, gave him a bit of advice on how he should've handled the situation. Quote from the Book:
" 'You should have told her differently' said Hermione, still with that maddeningly patient air.
'You should have said it was really annoying, but I'd made you promise to come along to the Three Broomsticks, and you really didn't want to go, you'd much rather spend the whole day with her, but unfortunately you thought you really ought to meet me and would she please, please come along with you and hopefully you'd be able to get away more quickly. And it might have been a good idea to mention how ugly you think I am, too,' Hermione added as an afterthought.
'But I don't think you're ugly,' said Harry, bemused. Hermione laughed."
I thought it was really sweet of Harry to say that he didn't think Hermione was ugly. And Hermione laughed...out of joy? Relief maybe? I really loved this scene.
(Seen and Unforseen)

When Cho and Harry fight over Marietta ratting out the D.A., Cho thinks the acne jinx of Hermione's to prevent D.A. members from blowing the group's cover was a horrible thing. Harry counters that he thought it was a brilliant idea. Cho gets angrier, retorting she forgot that "of course, if it was darling Hermione's idea--"
(Snape's Worst Memory)

Hagrid is leading Harry and Hermione through the forest to where Grawp is sleeping: "He (Hagrid) stopped suddenly and turned aroud; Hermione walked right into him and was knocked over backward. Harry caught her just before she hit the forest floor."
(Grawp) - sent in by Jessica

When Grawp tries to grab Hermione, Harry seizes her and pulls her behind a tree, where she clings to him, shaking and whimpering.
(Grawp)

Here's Proof #4 that Hermione's almost always in Harry's mind or is part of his mind (possibly the best proof yet).
Quote from book:
"The problem was that with just under a month to go until the exams and every free moment devoted to revision, his mind seemed so saturated with information when he went to bed he found it very difficult to get to sleep at all; and when he did, his over�wrought brain presented him most nights with stupid dreams about the exams. He also suspected that part of his mind - the part that often spoke in Hermione's voice - now felt guilty on the occasions it strayed down that corridor ending in the black door, and sought to wake him before he could reach the journey's end."
(Grawp)

In chapter 31, "O.W.L.s", on page 712, just before the break: "Harry turned over his paper, his heart thumping hard....Three rows to his right and four seats ahead, Hermione was already scribbling....He lowered his eyes to the first question: a) Give the incantation, and b) describe the wand movement required to make objects fly....Harry had a fleeting memory of a club soaring high into the air and landing loudly on the thick skull of a troll...smiling slightly, he bent over the paper and began to write." (I *Jessica* just thought it was cute that, for one, he noticed where Hermione was and what she was doing, and also, seeing her seemed to remind him of that particular charm, which is the reason he and Hermione are such good friends in the first place, along with Ron.)
- sent in byJessica

In the chapter "Out of the Fire," Hermione offers to sneak into Umbridge's office with him [so he can try to contact Sirius]. "...well then Harry, you and I will be under the invisibility cloak, and you can talk to Sirius.....I mean, you can check whether Sirius is at home or not while I keep watch, I don't think you should be in there alone..." Even through his anger and impatience Harry recognized Hermione's offer to accompany him into Umbridge's office as a sign of solidarity and loyalty.
(Out of the Fire) - sent in by Debbie

When Marietta was affected with the acne jinx after she snitched on her fellow D.A. s, Fudge asked Umbridge if there was a counter jinx since Marietta wouldn't talk and kept covering her face. Umbridge admitted that she had not been able to find one. Harry then felt a surge of pride in Hermione's jinxing ability.
(The Centaur and the Sneak)

Hermione's quick thinking saves Harry from Umbridge's intended Cruciatus Curse, putting on an elaborate act of fake confession that only Harry seems to be seeing closely enough to notice it's false.
(Out of the Fire) - sent in by Jessica

During his and Hermione's flight into the forest and the skirmish with the centaurs and Grawp, there are several instances of Harry protecting Hermione from injury or moving toward her instinctively in moments of danger... as well as yet another instance of Hermione's continued arm-grabbing. ;)
(Out of the Fire) - sent in by Jessica.

Quote from Book:
"'RUN!' Harry yelled, as the shelves swayed precariously and more glass spheres began to fall from above. He seized a handful of Hermione's robes and dragged her forwards, holding one arm over his head as chunks of shelf and shards of glass thundered down upon them."
Nice save, Harry!
(Beyond the Veil)

Quote from Book:
"Harry found the way ahead clear and saw Ron, Ginny and Luna sprint past him, their arms over their heads; something heavy struck him on the side of the face but he merely ducked his head and sprinted onwards; a hand caught him by the shoulder; he heard Hermione shout, 'Stupefy!' The hand released him at once." Nice Save, Hermione!
(Beyond the Veil)

Quote from Book:
"Harry saw the knees of the Death Eaters bend; poking his wand out from under the desk, he shouted, 'STUPEFY!' A jet of red light hit the nearest Death Eater; he fell backwards into a grandfather clock and knocked it over; the second Death Eater, however, had leapt aside to avoid Harry's spell and was pointing his own wand at Hermione, who was crawling out from under the desk to get a better aim. 'Avada -' Harry launched himself across the floor and grabbed the Death Eater around the knees, causing him to topple and his aim to go awry." WHEW! That was close. Harry literally save Hermione's life from the deadly Avada Kedavra curse!
(Beyond the Veil)

When Hermione is struck down by a Death Eater's hex, Harry's head fills with panic enough to keep him from thinking properly; kneeling beside her, he's overcome with guilt and fear (don't let her be dead, it's my fault if she's dead...), and a wave of relief powerful enough to make him light-headed sweeps through him when he discovers she's still alive.
(Beyond the Veil)

Here's the reason why Dumbledore didn't choose Harry as prefect. Quote from Book: "'I feel I owe you another explanation, Harry,' said Dumbledore hesitantly. 'You may, perhaps, have wondered why I never chose you as a prefect? I must confess . . . that I rather thought . . . you had enough responsibility to be going on with.' " See? So, if the circumstances had been different, Harry and Hermione would've been prefects.

Quote from Book:
"Harry looked around. Cho was passing, accompanied by Marietta Edgecombe, who was wearing a balaclava. His and Cho's eyes met for a moment. Cho blushed and kept walking. Harry looked back down at the chessboard just in time to see one of his pawns chased off its square by Ron's knight. 'What's - er - going on with you and her, anyway?' Ron asked quietly. 'Nothing,' said Harry truthfully. 'I - er - heard she's going out with someone else now,' said Hermione tentatively. Harry was surprised to find that this information did not hurt at all. Wanting to impress Cho seemed to belong to a past that was no longer quite connected with him; so much of what he had wanted before Sirius's death felt that way these days . . . the week that had elapsed since he had last seen Sirius seemed to have lasted much, much longer; it stretched across two universes, the one with Sirius in it, and the one without. 'You're well out of it, mate,' said Ron forcefully. 'I mean, she's quite good-looking and all that, but you want someone a bit more cheerful.' 'She's probably cheerful enough with someone else,' said Harry, shrugging." So what's so significant about this quote you say? Well, for one, Harry's no longer interested with Cho which is probably the start of my dream theory on the transition from Cho to Hermione. Next, it all came out from Ron's mouth: "you want someone a bit more cheerful." Here's the thing. Hermione's Patronus is an otter. Patronuses sort of reflect on their owners. An otter, it seems, symbolizes Joy, Playfulness, Sharing, Feminine Power, Helpfulness, Sharing, Adventure, the Magic of Joy, Youthful Exuberance, Zeal, Laughter, Curiosity, Mischievousness. All that translates to cheerfulness. It's a long shot, but hey! At least I found a connection.
(The Second War Begins)

Observation: Although it's Ron and Hermione who end up prefects - and therefore who you'd expect to spend a lot of time alone together - it's Harry and Hermione who end up spending most of their time together. Almost all the major scenes show the two together, and even the littler ones.

Observation: This book also debunks at least three prominent anti- H/Hr arguments - that Harry finds Hermione unattractive, that any time they spend on their own together is grating for both of them, and that Harry wouldn't feel left out with Ron and Hermione spending time alone together.

Observation: The two major things that alleviate the steady crumminess of Harry's school year, the D.A. and the Quibbler interview, are both due to efforts of Hermione's.

Observation: JKR has continually stressed on how Hermione is a part of Harry's mind here in the 5th installment: 3 times in fact (4 if you include the one from GOF)

Observation: Just as she did in the 3rd book, JKR put Hermione, Harry and Buckbeak in one place (though it's just a single scene). Remember that the Hippogriff's a symbol love. Harry (when with Beaky) is never shown together with other people (okay, maybe Sirius but I'm talkin 'bout the opposite sex) other than Hermione and the same is true for her. Hmmm...."
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