There is a lot of background in this chapter, so please forgive me if it reads a little slow.

Flying Lessons, Chapter 2

John walks back into Elizabeth's quarters the next morning and finds her in virtually the same position that he left her in last night. She's still wearing her uniform from the day before and hasn't bothered to take off her shoes.

Elizabeth stirs when he sits on the edge of her bed. She turns toward him, but buries her head under the pillow with a groan when she sees him wearing running clothes.

"No you don't." He pulls the pillow off her head. "Come on, Legs. Get your ass up."

"Unh-uh. Don't wanna." Her arms have come up to replace the pillow and she is trying to dig her face into the mattress. He wonders how she's managing to breathe – better to be safe than sorry.

John grins and pokes his fingers in the spot just above her hip. This causes Elizabeth to squeal and jump up to a sitting position. The glare she gives him would be deadly if she wasn't so rumpled.

"Come on. You've been asleep since 17:00 yesterday. That's plenty. Go get dressed before most of Atlantis gets up."

Elizabeth grumbles something unintelligible, but gets up and goes to the bathroom attached to her quarters. She's out in a few minutes wearing her running clothes with her face freshly washed and hair slightly damp. They walk out of her quarters together and start their usual route down to and through the lower levels of Atlantis.

Their runs have become a bit of a ritual whenever she doesn't have early briefings and he's not off-world. Being at the top of Atlantis Command gives them access to all of the sleeping quarters. This makes it easy for one to help provide motivation to the other if it's needed. If anyone else in Atlantis finds it strange to see them walking in or out of each others' quarters in the early morning hours, nobody has approached them about it.

It had taken Beckett a few weeks to clear her to run again after her emergency surgery. Sheppard was waiting for her that first morning. She had quirked one eyebrow, shrugged, and started to run. He followed.

It was on that first morning, their first run together, that he had come up with his nickname for her. Elizabeth was fresh out of her recovery, so even a short run had made her very winded. John had claimed, between loud guffaws, that there was no way he could call her "Elizabeth" or "Dr. Weir" when she was dripping with sweat and panting like a dog. Deciding on the spot that none of the standard nicknames associated with Elizabeth fit her, he started calling her "Legs". She had been too busy trying to get enough oxygen in her lungs to protest. He never uses it in front of other people because he assumes, correctly, that he would then be forced to stop using it all together.

By unspoken agreement, they run in silence, using the time for inner reflection even though the company is appreciated. She has laughingly called it being alone together. Their conversations don't start until they've come to a stop on one of the balconies to catch their breath and stretch. It's very rare for these discussions to center around work. They usually talk about random things like their childhoods or old TV shows or to gossip over the constant merry-go-round of dating in Atlantis.

They have slipped into an easy friendship since their day at the island. She still works too hard and he does everything he can not to take anything too seriously. He continues to flirt outrageously with all the women he meets both in Atlantis (which she is sometimes witness to) and off-world (which he knows that Ford or McKay love to tell her about). Elizabeth teases him about it, sometimes calling him "Kirk" and he figures that is slightly better than "man-slut" – that is what she calls the character when they watch one of the many Star Trek episodes that have been downloaded into the main computer.

Elizabeth tells him that he won't ever stop. That he'll be picking up on his grandsons' dates when he's old and gray. John knows she's probably right. There's something about the start of the chase that he has always enjoyed. It's like taking off in a new experimental plane – while the entire flight is exciting, it's the take-off that leaves your heart pumping.

Elizabeth doesn't know that he never follows through with all flirting. John doesn't tell her that he pictures his grandsons looking like him, but imagines them speaking 6 or 7 languages - including Ancient. That thought should really freak him out, but it doesn't. And he's not the type of guy to over analyze stuff like that.

At the end of their run this morning, he is fairly sure he knows what she'll want to talk about. He waits until she's ready.

"Last night wasn't a dream, was it?"

"Nope."

"That's what I was afraid of."

"Why does the chair freak you out so much? It's actually pretty cool."

"I've seen the destruction that O'Neill was able to accomplish by sitting in a chair like that. Just it's existence scares the hell out of me. The fact that I may be able to control it isn't something I can put into words."

"But it's a defensive weapon."

"It's still a weapon."

"A weapon meant to protect the city."

"A weapon that almost blew you out of the sky not so long ago."

"Well...yeah..."

He didn't have a good answer for that. Even a defensive weapon is dependent on who wields it. Beckett could have killed him and General O'Neill. But if there is anyone on Atlantis he trusts more than himself with this weapon, it's Elizabeth.

"You've been worried about how we'll defend Atlantis against a Wraith attack. Now we probably can."

"I just never thought I'd be the one directly responsible for that defense."

"Well, I never thought that I'd be in another galaxy fighting soul sucking vampire things either."

"So you're telling me to suck it up and stop complaining."

"Pretty much."

Elizabeth sighs and rubs her hand over her face. She still looks tired.

"Look." It's time for him to try a different tactic. "There's more to having the Ancient gene than sitting in the chair. I'll show you."

John stands and holds his hand out to her. She hesitates for a second, then lets him help her up. Once she's standing, she narrows her eyes at him suspiciously.

"You're not going to make me wear a shield so you can shoot me, will you?"

He laughs. "No. And I'm not going to throw you off a balcony either."

"Promise?"

"Promise."

John leads them out and through the hallways of Atlantis. When he doesn't take a left at the proper corridor to their quarters, she looks up at him questioningly.

"We're not even going to get cleaned up?"

"Nope."

"Okay."

Elizabeth continues to follow him, but comes to a stop at the door into the Jumper bay.

"John..."

He gives her a grin and motions his head towards Jumper 3.

"Come on."

She doesn't move, so he walks over and grabs her by the elbow. He pulls her into the bay and toward the Jumper.

"John..."

"Don't John me, Legs. I know you've got a secret desire to be a Top Gun."

John corrals Elizabeth into the Jumper as the doors above them open to show beautiful sky. He puts her into the pilot's seat and places her hands on the controls. The ship comes to life instantly. She looks over at him with wide eyes.

"Are you really going to make me do this?"

"Oh yeah."

He settles into the other seat and flashes her another grin.

"Let's get going."

John watches Elizabeth close her eyes and take a deep a breath. He sees the look of determination when it takes over her features. She gives him one final look and he nods. The Jumper slowly rises into the air. Elizabeth swallows when she sees the city and the water below them.

"Okay. Now nice and easy. Relax and just think of where you want it to go."

This isn't the first time John has taught someone to fly a jumper. If McKay could learn, then so could Elizabeth. She takes another breath as the craft starts out over the water. They accelerate slowly as Elizabeth gets the hang of controlling the Jumper.

"Let's lose a little altitude."

The jumper drops smoothly towards the water.

"Okay. How about a turn?"

Elizabeth executes a perfect right turn and the motion pushes John into the side of his seat. He realizes just how fast they are moving over the water. He looks over and she flashes him a grin.

"Let me guess, you were a lead foot back on Earth too?"

"More tickets than I care to talk about, thank you."

He leans back with his arms behind his head and laughs.

"So...where are we headed?"

The display appears in front him, making his smile broaden. The flight plan goes out away from Atlantis and seems to stop over empty water. But he knows that area isn't empty. He is just starting to think that this is going to be a great morning, when a voice comes out over the radio.

"Major Sheppard. This is Atlantis command."

"This is Sheppard," He responds with a sigh.

"We cannot seem to locate Dr. Weir."

"I'm here Peter." John is hoping he's not imagining the sound of disappointment in her own voice.

"Dr. Weir - Sgt. Bates and his team are back. They seem eager to report."

Elizabeth raises an eyebrow at John and he shrugs. He doesn't think he could ever use the word "eager" to describe the usually over-stoic Sgt. Bates.

"Okay Peter. Major Sheppard and I are heading back now. Please tell Sgt. Hughes and his team to report to the infirmary. Briefing in a half an hour."

They weren't too far from Atlantis, so John knew that Elizabeth was giving them time to get cleaned up before the briefing.

"So. How fast do you think you can get us back?"

Sheppard immediately regrets his challenge when he's thrown into the back of his seat. Only Elizabeth's peal of laughter next to him softens the blow.