A/N: To keep things clear. Italics are character thoughts. Also I just couldn't stand going on with the sequel until I edited this fic for errors both in wording, grammer and storyline. I haven't changed much of the storyline but I have made the ending semi-open for the sequel. Your welcome to re-comment on my live journal account's posting of Going Commando. See my profile for more details.

Title: Going Commando

Author: Lady Valmar

Genre: Humor, Suspense/Mystery

Rating: Mature (due to later chapters)

Archive: FF, SGAHC, FB

Beta: None (Feel free to volunteer peeps)

Spoilers: Set in Season 2 with some reference only to a Season 3 episode.

Date: Unknown

Sequel: Burden (It's a working title right now)

Summary: This is just plain wrong. Evil plot bunny I swear… okay all I'm gunna tell you is think of Sheppard and the word commando in the same sentence and that should tell you something.

Warnings: This is so wrong, I am warning you know, But the evil plot bunny attacked me while I went through something similar to this. Don't worry I wasn't seen thankfully like Sheppard is. LOL! Okay from chapter 5 onward I start getting more intense with my adult themes. This does feature John getting raped though I do not go into full description of the event. Just bare with it my dears, you won't be disappointed.

Disclaimer: I don't own Stargate Atlantis or any of the characters, So stuff not owned by Stargate Atlantis is mine and therefore please ask and do not infringe nor steal my original themes, concepts, ideas or characters please.

... .LV. ...

Going Commando

By Lady Valmar

4:30 am

Waking up to the sound of your alarm screaming into your ear is one thing another is to take a smack at it and have it fall down on your head while your half-asleep. Sheppard rubbed the side of his head, where his blasted clock had fallen and hit him. He just knew he shouldn't have bothered with setting up the clock in his room, let alone bringing it with him to Atlantis, still old habits die hard, he guessed.

It had been a ruff few days and the thought of just relaxing made him take a deep breath. Today wasn't going to another one of those run around days, where he did reports, played guinea pig to Rodney or worked with those few men under him who needed some extra training. No, today was just another lazy, put your feet up days.

Now if he could only get that throbbing dent in his head to calm down he could figure out what he was going to do.

John rubbed his head and yawned. It had been a late night, he'd swore to himself that last night he was going to get some sleep but then his laptop had been acting up so he'd gone down to Rodney's lab. Boy that had been a mistake. Rodney went on endlessly about using the scanners he'd installed in John's laptop since the last crash.

When John told him that pushing the power button was just as efficient, Rodney had gone into his computer-geek mode. It was the mode where he lectured John on what not to do with his laptop and why. By the time he'd got back to his room it had been 2:30 am. Now he was awake and there was no going back to sleep.

It wasn't hard to get to sleep, it just he sometimes had a hard time convincing his mind that it was time to shut off. Looking down at the offending object in his lap, he shook his head. It was time to invest in one of those watches…the kind that set to Atlantean time.

After he had sat the clock back on the table near his bed, he sat up and stretched lazily. Well it was time for his daily run with Ronon, then on to practice with Teyla. Flinging back the covers, he set both his feet on the floor, and that was when the next terrible thing to happen was his feet touching something wet… A very sticky, wet something.

Frowning, he looked over only to see his water glass sitting on the floor on his shoe and the stuff that had been in the glass was dripping from his mattress. The best part was that his covers had seen a taste of the action too, as he had a habit of doing wild kicking maneuvers while sleeping sometimes.

"What the hell!" John growled. He figured that he'd been so tired last night, that it was possible he might have just feel asleep with the glass in hand or sitting on the bed. Not a normal thing he'd do, but then this past week had been anything but normal.

Standing up, he snatched the wretched glass, so much for a lazy, put your feet up day. Sheppard glared and felt a slight breeze as the air controls turned on to adjust the room temperature.

"That's funny…" He remarked before looking down at his underwear.

Well so much for those pair…he thought, dropping his boxers, which slopped in the same pile as the soaking sheets. There wasn't much he could do for the mattress but thankfully the offending liquid hadn't soaked too much into it. The covers didn't really matter all that much. He could travel down and get some fresh ones from supplies, hopefully.

He pulled the covers into his arms and went into the bathroom, which had two racks and hung the covers on it. There was no point in re-washing his boxers if it was just water, it would dry. The problem was it wasn't just water, it had a type of flavoring in it that had the noticeable characteristic of staining stuff, if left untouched.

Sheppard had been introduced to this flavoring by Teyla, who said that Athosians used a grounded up herb called Curash, which added a minty flavor when added to water. It seemed to be the Earth equivalent of catnip, in that it had much the same properties in that it helped with a dry throat or stomach problems, both of which Sheppard had been suffering from last night.

Glaring at the water glass, as if daring it to say something to him, he walked over to the laundry hamper and deposited his boxers. Belatedly, he realized that all his laundry needed to be washed. Standing for a moment still stock naked, he realized that maybe he'd better shower first. The stuff was making his skin a little itchy.

He deciding it might be best to radio Ronon and let him know that the daily run was off the menu for today. Just in case he reminded himself if he got hung up with his laundry he'd have to call Teyla and also cancel their practice session. After he'd finished with a short radio conversation he traipsed off to his restroom.

Jumping into the shower he scrubbed for a while and when it wouldn't come off, he used the more potent lava soap he'd been given from the maintenance department awhile back. It did the job well. He scrubbed every spot the blue covered and afterwards, he briefly washed his hair. There was no point in all this showering without actually washing the rest of him.

Grabbing a towel, he dried off and began to look for a fresh pair of boxers in his drawer. A what a surprise…no underwear. Sheppard frowned. Well if he couldn't find any clean ones he might as well, use a dirty pair, at least until his laundry was done. Walking over to the hamper, he pulled out the wet, blue pair, nope!

Next he pulled several grimy towels off and felt his frustration grow. Two pairs were soiled with dirt and grim…the last things he wanted to wear. Then he had found a pair he had the luxury of smelling a musky odor and on further inspection seeing his own emission…on. Those pair were definitely off the list.

The last pair he had found had some odd green stain on them…that he didn't even want to know how it had gotten there. Chucking everything back into his hamper, he sighed. If there was ever a day to have no clean boxers to wear or even dirty ones to wear, this was the day. Sheppard frowned. He never went out without boxers but today was looking like he would have to do exactly that.

As he eyed the wet boxers, his com beeped at him. Talk about bad timing.

It was McKay's voice and from the sound of it he wasn't happy.

"Sheppard respond!"

Walking over to the com, he put it in his ear. "Yup."

"Yup…what the hell is yup for. Where are you?"

"Where do you think, in my room."

"Don't you usually go for a run with Ronon on your days off?"

"Yeah well…got a little side tracked at the moment."

"Side tracked?"

"Yes! Now what do you want McKay?"

"I need you…erm…I mean your gene."

"Oh really?"

"Yes…mine won't cut it."

"And may I ask why not?"

"Because it just doesn't alright. Now come down here Sheppard, it's not like your busy at the moment."

Sheppard looked down at his naked body, so not busy huh…. He really needed to do his laundry sooner.

"Well…when you put it that way…say please."

"What!"

"You heard me McKay. I'm not your personal servant, now say please and I might just be nice enough to meander down to your lab and let you use my 'gene' as you are demanding of me."

That reminds me I'd better radio Ronon after this and see if he's up or if he's already done the morning run.

"I will do no such thing. Now come down here Sheppard!"

"Jeez, pushy. Are you in a bad mood? Didn't get your morning coffee did you?" John snickered, that should do the trick. He really knew how to push Rodney's buttons.

"Oh shut up…for the love….okay fine…please."

Sheppard smiled. Bingo! About time McKay was polite.

"Please what?"

"If your trying to make….ahh….help…oh my…."

The radio went dead with static. Sheppard shouted into the com, "McKay? McKay? Dammit Rodney!"

Racing to his chair, he yanked on his shirt, put his pants on, then his boots. Then putting on his belt and holstering his gun, he raced down to Rodney's lab. When he got there, he couldn't help but begin to laugh. The scene before him had, Rodney glaring at some type of device, with him muttering curses at it as he glared at his hands. On his left hand side, was one of McKay's female staff technicians, her face scrunched up in a vicious grin.

"Way to go Dr. McKay," she shouted, clapping her hands together.

Sheppard started to laugh more as he saw McKay's hands. They were pink to be exact. A bright neon pink. "So I'm guessing don't need my help after all? Unless you want me to help you get some makeup from Elizabeth to match those pink nails Rodney."

Rodney turned around, his face flushing a little red and glaring at Sheppard in spite of it. "You can…uh…"

"What Rodney? I've got some lava soap that might do the trick unless this is permanent, in which case, your going to have a hard time living this one down buddy."

As he was about to comment on Rodney's expression he stopped, as he caught sight of the assistant walking alongside Rodney and just blatantly staring at his crotch. To make matters worse Rodney's expression had changed to a look of horror. Then as he watched Rodney's eyes turned upward quickly while the tech's stayed connected to his crotch. He couldn't believe it, she was just staring, deadpan.

"Something wrong?" Sheppard asked, having a bad feeling that it had something to do with his pants. "Oh no it's that blue color, it's on my pants isn't it?"

When either of them didn't say anything, he gagged that the blue stains were not what had Rodney turning his eyes up at the ceiling, a horrified expression on his face and the woman's face turning red "What is it? Rodney!"

"Your…fly…it's ah…unzipped…and ah…" said the tech timidly.

He swallowed slowly and flushed as he looked down to see his fly open and a bit of his pink flesh showing. Panic erupting, he turned around and zipped up quickly, only to bite his tongue in the process.

Turning back slowly, after he'd composed himself he breathed in deeply. Okay what should he do? Run or say something or nothing at all. Finally when the door whooshed open in the background to another lab he found the courage to look up and saw a giddy look on the tech's face.

"So…ah…you go Commando huh?"

A/N: Hopefully this version is even better, if you have already commented and still wish to comment on the new version just comment on my livejournal for all previous version updates to chapters. I do hope that made sense. For anyone new to this fic, it's going to sound funny but soon enough you'll see… Poor poor John. The things we writers love to do to him.