Author's note: Ok, this is totally not my usual ship but I was watching The Seed earlier and this little plot bunny just popped into my head. Sheppard just seems to watch her a lot in this episode and it got me thinking.

Disclaimer: I own nothing, please don't sue.

Spoilers: Through mid- Season 5, mostly The Seed, First Contact and the Lost Tribe.

A Surprising Affection

It had started slowly. He hadn't even known it was happening at first, though in hindsight, it all seemed so obvious. It was concern that she was stressing over her new role as CMO, gentle reminders to get some rest or sticking around for an extra few minutes after getting checked out to hear about her day.

The idea that it might be more serious only came after the quarantine. He knew that something had happened with her and Ronon and the twisting in his gut shocked him into some much needed self reflection. He was coming to care for her, he realised. Somehow, the lithe blonde doctor had wormed her way past his defences and set up a little residence somewhere in his chest which was remarkably close to his heart.

He swore to himself that she was just becoming part of his team, that he looked after her like he would anyone on Atlantis. Convinced himself in his moments of doubt that even if there was a spark of interest there that it should go unexplored. He saw how Ronon looked at her now, the affection in his gaze, though it seemed that the quiet Satedan was unwilling or unable to recognise the depth of his feelings for Jennifer. John knew from what little Ronon had said of his past that this was a huge step for him, an opportunity to love again which John would not dream of taking away.

So he kept quiet, buried any lingering interest and focused on the missions at hand, defeating the Replicators, finding Teyla, defeating the Wraith, protecting the city. There certainly was no shortage of distractions.

But something had changed in the last week, and the spark had come roaring back to life. She had awakened Carson from stasis, glowing with happiness, yet obviously exhausted. She had been pushing herself too hard he realised. He had urged her to get some rest, staring after her as she left the room. Suppressing his worries, he turned back to his team and plastered a smile on his face, pleased that Carson was with them once again.

The panic he had felt the following morning as he rushed into her chambers was unlike any he had known for years. Sure, he had worried about his team and the people on Atlantis but this panic was deeply personal, like he was loosing someone integral to him. She just lay there, unable to wake up, to respond, tied down by mysterious growths. He could barely restrain himself from loosing it, he was desperate the rip her free and never let her out of his sight again.

The following days when she had been turning into a hive ship were some of the worst of his life. Not only was he loosing Jennifer bit by bit, but he was fairly certain he had given away his affections for Jennifer to Ronon and he was not entirely sure the big guy would forgive him this particular trespass.

When Woolsey had explained the extent of the ship's growth, the treatment options and then suggested the surgical strike it had taken all his willpower not the lash out and beg him to find another way to bring Jennifer back. John was fairly certain his reaction had slipped past Woolsey and Rodney but Ronon was more observant than most. He hadn't said anything but had been watching him with suspicious eyes ever since.

That had been nearly three months ago now. Jenn had gotten better, and John had buried himself in his work, desperate to ignore the way her smile tied his stomach in knots. He had nearly lost her again twice, first to Kiryk and then to the Wraith on the Daedalus. Both times Ronon had been there to save her, leaving him both grateful for his presence and resentful of their increasing closeness. Ronon's affections were no longer a secret . He was now actively pursuing the doctor, who seemed to welcome his advances, John noted bitterly.

The Daedalus had landed just a moment ago and while John knew she was safe, he was desperate to confirm with in his heart what his head already knew. He had to see her. Walking quickly along the corridors, he slowed as he heard Ronon call out to her. Not wanting to intrude but unwilling to leave without seeing her, he waited quietly in the shadows, listening to a conversation not meant for his ears.

"Dr Cole's taking my shift, yeah."

"Want to get something to eat?"

"Um… listen… eugh… I'm really glad you came on the mission. Without you there we'd probably all be dead. But I just want to be clear, because umm… I just want to you know that I'm kind of interested in somebody else."

"So?"

"I just didn't want to give you the wrong…"

"You didn't. I just wanted to get something to eat."

"Okay… because I though that…"

"Yeah well, you're wrong."

"Okay.

"Okay."

"Do you still wanna go…"

"Ah, no. I should… I should probably…"

Eavesdropping hadn't been his intent and now John didn't know what to do with the information laid at his feet. On one hand, he was pleased that the Doc didn't seem interested in Ronon. Yet, he knew Ronon cared for Jenn and wanted him to be happy. And yet another part of himself was enraged, desperate to know who this 'somebody else' she spoke of was.

Waiting until Ronon stormed past him, clearly too upset to realise he was there, John peaked his head around the corner to see Jenn still standing in the middle of the hallway, looking lost.

"You ok Doc?" he asked, unsure of whether or not to let on about what he heard.

"What… yeah, just… I'm fine." Finally looking him in the eye, she put forward a strained smile and inquired about him, "how are you? Did I miss any excitement on Atlantis in the last few days?"

"Not much. Just Rodney and Zalenka fighting again, nothing new. Seems like you guys got to have all the fun out there on the Daedalus."

"Ha. Only you could qualify that sort of harrowing experience as fun!" she laughed.

She was ok, she wasn't in love with Ronon and she was standing here with him. John couldn't keep a grin off his face as he held out his arm and with a laugh, asked is he could have the honour of escorting the victorious heroine to her chambers for the night. Laughing, she agreed, slipping her hand into the crook of his arm.

The walk to her chambers was a pleasant one, filled with banter and leaving John feeling calmer than he had been since she had gotten on that damn ship. He may not be able to tell her but the worry had been eating at him. Now that she was back, safe and whole, he wanted to leap for joy, twirl her in his arms and taste the sweetness of her lips.

Reaching her door, they stopped, both becoming uncharacteristically quiet.

"Well here we are" she said shyly.

"Yeah… well, anyway Doc, glad your back safe and sound. Sleep well" he said before reaching down to give her a quick hug. He was surprised when she return the hug, hands fisting in the back of his shirt unwilling to let go.

"You sure your ok Doc?" he asked, gently reaching his arms around her to rub soothing circles on her back.

"Yeah, I just… the trip was scary and then when I got back…"

Ah, he though, "the thing with Ronon you mean?"

"You heard that huh?"

"Sorry. I didn't mean to, but didn't want to interrupt either."

"It's ok" she said, blushing furiously. "It's just, I hate that I hurt him."

Trying to be unbiased and sympathetic, he told her, "as long as you were honest with him, that's what matters. It would have hurt more if he found out later."

Sniffling, she mumbled incoherently into his shirt. "you were honest with him weren't you Doc?" he asked, terrified of the answer.

"Yeah, I was. The someone else, well its them I'm worried about. I don't have a clue if he feels the same way."

"Can I ask who he is?"

Taking a deep breath, she decided to take the plunge and lay her heart on the line. "You."

Pulling back in shock, he held Jenn away from him so he could look in her face. "Me?" he asked incredulously.

"Yeah" she mumbled, blush spreading across her face and down her neck, and beneath her shirt. Shit Sheppard, don't go there right now, he thought.

"Oh"

"I'm sorry, I shouldn't have said, I'll just go." she mumbled, pulling away, taking his silence as an embarrassed rejection.

Panicking as she tried to pull away, he yelled, "no!" and pulled her back against his chest. His heart was beating a million miles an hour. She was interested in him! Holy shit! How the hell did this happen? When? Realising he had been silently holding her for the better part of a minute, he took a deep breath, steadying his thoughts to respond. Looking down into her eyes, he said, "Don't go. I… I'm not much good at this, feelings and relationships I mean. But I… Jenn… I really care for you. I want to try for you."

Her eyes softened at his words, and she reached her hand up to cup his cheek. "I want to try with you John. If you'll have me."

"Always" he smiled, gently lowering his head. He stopped, just a hairs-breath before reaching her lips, allowing her the option of pulling away. Without any hesitation, she closed the gap, pressing her lips to his, igniting his senses in a cacophony of sounds, tastes and smells. John had always thought the metaphor of fireworks had been too cheesy to be real, but right now, kissing this woman, it was all real. She stole his breath and gave him life, softened his rough edges and awakened the needy, lust-filled beast within. It was a mess of contradictions, a yin and yang, opposites in perfect balance. She was the future he had fought against for so long, and now with her in his arms, her body pressed against his, he couldn't remember why.

Pulling away gently, as the need for oxygen became paramount, he rested his forehead against hers.

"Wow" she said, smiling.

"Yeah."

"You want to come in?"

"Definitely." No more half measures, no running, there was nothing that was going to keep him from her side ever again.

The End