There isn't much to say regarding why she left in the first place. You could say it was relationship troubles, or team troubles, you could say it was the guilt she experienced from taking the cure, or even all the dying and loss they'd all gone through in such a short amount of time... it wasn't any one thing as far as she could tell.
Besides, the reason why she left was never really that important anyways. What kept her away... now there's the million dollar question.

Like anyone would be
I am flattered by your fascination with me

In her defense, she was just staying true to her name. She was the black sheep of their pseudo family, and it was just a matter of time before she acted on it. Nevertheless, it's all water under the bridge now. Her time away has served her well, and she's feeling confident enough that three years away should take care of such silly childish behaviour.

So they all smiled at her and welcomed her back like she's the prodigal daughter who's come to her senses. They pulled out the good china for dinner and celebrate her return as if none of them are bothered by her flippant attitude towards her leaving in the first place. Everyone that is, except for him. The very thought of him sends shivers up and down her spine in such a delightful way. You'd think three years was long enough...

Like any hot-blooded woman
I have simply wanted an object to crave

Of course she should have expected nothing less from him. It was always something she'd admired about him, the way he didn't feel the need to lie to make anyone feel better. Blunt, direct and to the point. In any other situation, he was nearly impossible to read, but in this given circumstance, his feelings on her return were pretty obvious. He was pissed. His silent, astute stare was proof enough of that.
After dinner, she was graciously shown to her room before she was left alone with the privacy she'd been itching for. And now she's alone, staring out the window to the view down below that was once so familiar to her. Back when she was just a kid.
With a deep breath, she reaches over and turns on the dim desk lamp that sits next to her bed before turning around to start the tedious chore of unpacking.
"You should lock your door y'know."

But you, you're not allowed
You're uninvited
An unfortunate slight

Her head snaps up and she squints at the man suddenly standing in her open doorway. "You talkin' to me now?" She asks, moving over to the suitcase on her bed. She knows it's ridiculous of her to act this way, but she could feel her stubborn attitude urging her on. Besides, he used to like that about her.
He crosses his arms and leans on the door jamb with a grunt. "I could say the same to you."
"How do you figure that?" She unzips her suitcase and flips the top off, not really interested in hearing his answer.
"Three years with no Goddamn word?" He cocks an eyebrow cynically.
"I was busy." She shrugs, feeling herself tense up uncomfortably under his stare. "Besides, I'm sure you hunted me down at least twice in that time. Just to check up. Am I right?"
His stare grows hard and he squares his jaw. "You don't know how to stay outta trouble. Don't act like you don't like someone watchin' over you."
"I don't! I appreciate your concern for me, but I don't need a brood of mutants watching over me like some... twisted gaggle of guardian angles." She rolls her eyes with an aggravated sigh. "I'm sure the X-men can find better use of their time."
"No one said anything about the X-men."
"What does that mean?"
She can hear his low throaty growl from all the way across the room. Ignoring his unspoken, rumble of a threat, she crosses her arms expectantly and waits for her answer. After a long tension filled moment, she turns back to her luggage, resigned to accept his lack of response.

Must be strangely exciting
To watch the stoic squirm

"You don't have to do me any favours." She snips as she idly organizes the clothes inside the bag. "I'm a big girl."
So what kept her away?
You could say it was because of their lopsided relationship. The one where he saw himself as her big brother, and she saw him as... nothing of the sort. Not even close. Three years should definitely have taken care of that.
He lets out a deep breath, which she can only assume is in an attempt to cool his jets. "You leave in the middle of the night without a damn word to anyone, and that's it?"
"Said the pot to the kettle." She mutters before looking up at him with a frown. "Is this the only reason you came up here? To pick a fight with me?"
He clenches his jaw and shoots out another sharp breath before stepping into her room and shutting the door behind him. The way he used to do when he was about to give her a piece of his mind and didn't want the rest of the nosey residents listening in. She waited for him to start, hearing the usual dialogue run through her mind like an old tape. He'd tell her it was a stupid thing to do and that she was just a kid. Or he'd say she could have been hurt, or tell her how terribly irresponsible it was. Because clearly, he was the first person she'd think of to judge good responsibility.
But instead, he said nothing. She swallows hard again, suddenly feeling anxious and awkward, wondering what the hell he was staring at her like that for.
"I didn't come up here to fight, kid."
She blinks at him, patiently waiting for him to elaborate, watching as he shifts his weight from foot to foot and clears his throat.
"Come on, you know I'm no good with words."
Her eyebrow perks up and she internally relaxes. "Is this your way of you're happy to see me?"

Must be somewhat heartening
To watch shepherd meet shepherd

"Yeah." He shrugs. "I guess. We all are."
She steps towards him, her brow pinched and her hands twisted together anxiously. "Well it's good to see you too. It's good to see everyone." She adds with a shrug.
"We were all pretty worried about you kid." He grunts as he watches her walk towards him. "It's good t'know you're doin' okay."
The corner of her mouth curls up slightly despite her knit brow and she nods, coming to a stop in front of him.

But you
You're not allowed

"Yeah, I'm okay." She says softly, pressing her lips together into a half hearted smile. "I really missed everyone."
"You shouldn't have stayed away so long." He frowns, reaching up to playfully tug the white strand of hair that hangs loosely against her cheek. His hand grazes her flesh and he lingers a bit. She bites her lip hard, hoping that it'll help distract her from how amazing it feels to have him touch her. Even in such a trivial way.

You're uninvited

Something in his expression changes. She can't tell what it was exactly, but he squints at her slightly and frowns. She can't help but notice that his hand is still burning a hole into her left cheek.
"What's yer problem?"
She casts her eyes downward and shakes her head, embarrassed that he picked up on her delight, even though he doesn't realize that's what it was. And now she's blushing, adding to her mounting horror. There's no way he'd miss the sound of her racing heart beat.

An unfortunate slight

"Nothing." She tries to say as casually as possible, still avoiding any eye contact as she wishes he'd just take the hint and leave. He doesn't. Instead, he slips a crooked finger under her chin, lifting it up gently to make her look him in the eye. Her heart thrums against her chest the instant his flesh makes contact. She stares at him, watching his expression shift from concern to eventual realization.
And all he manages to say before she finally gives in to her inner voice screaming at her is
"Rogue,"

Like any uncharted territory
I must seem greatly intriguing

She grits her teeth and sucks in a breath before closing the space between them, crushing her lips against his as she slips her hands into his hair to pull him closer. She drinks-in the intoxicating taste of his lips, relishes the feel of her body pressed up against his, trying to memorize every last tiny detail of this moment, knowing that at any second he's going to come to his senses and jerk away.
He tips his chin up, removing his lips from hers. She leans her body even further into him as she watches him hold back, making a sound in the back of his throat that can only be described as a growl.

You speak of my love like
You have experienced love like mine before

His eyes shift down to meet hers again, and even in the dim light of the room she can see that they've darkened considerably.

But this

He dips back down, capturing her mouth in his hungrily as he twists his arms around her waist, pulling her in even closer.

is not allowed

She wraps her arms around his neck, dragging her nails through his hair with a breathy moan.

You're uninvited

She drops her head back, arching her spine as he makes his way down her neck, contorting his body to stay true to hers.

An unfortunate slight

She catches his lips again and he groans, reminding her of the sound a purring lion would make. His hands move down the curve of her back, ease over her hips, coming to a stop on her backside and she tips her chin up to deepen the kiss. He twists them around so she's pinned against the wall, their breathing heavy and ragged as his hands roam about her body. Her flesh tingling from anticipation when he lets out a heavy rumbling breath, placing a hand against the wall on either side of her and pushing back slightly so he's hovering over her. She forces down a swallow, feeling her breath hitch in her chest as she stares at him.
"Logan?"
He silently stares at her, breathing heavily with his mouth drawn into a tight line.

I don't think you unworthy
I need a moment to deliberate

A/N: This songfic was brought to you by the Letter "K" and the Number "C" (huh?) No but seriously, it was produced for the I HEART ROGAN random sonfic challenge run by JohnPaulGeorgeandRingo! (This is just one person, not literally all of the Beatles.) So if you enjoyed it, why not head on over there and check out some more?! YAY!

Also, I'm not very good at songfics, but feel free to leave your two cents. Or three. I'm not picky. (But I am HILARIOUS! Hahaha... sigh.)

A special thanks to Starlight2twilightfor bolstering my self esteem with her brutalhonesty (beta reading) and to spell-check, for pointing out my many flaws to which I had no former knowledge of. (I spelled hilarious wrong. WTF?! I totally can't spell.)