Title: A Cloud Across the Moon
Rating: MA
Author: Prothrombintime
Beta: riftintime
Synopsis: What if Ianto were in charge of Torchwood Three, and Jack was still a rogue freelancer? A canon-based Torchwood AU.
Disclaimer: Torchwood belongs to the BBC. I don't own anything. Just having fun.

Author's notes: This story will be quite different from "What is Essential…" Just wanted to try my hand at mixing things up after spending so long adhering strictly to canon. I will probably post once a week. There is another story currently posting called "A Good Man" by pennysstuff, which also has Ianto as head of Torchwood. The two stories are unrelated, and any similarities in the premise were completely coincidental and unintentional.

Acknowledgement: A special thanks to riftintime, an immensely talented writer, a fantastic beta, and a dear friend. riftintime gives me endless support, advise, suggestions, ideas, patience, encouragement, and kicks my prose into shape.

Chapter 1

Ianto Jones, leader of Torchwood Three, Cardiff, rose from his wooden chair, dusted off his already immaculate trousers, straightened his perfectly knotted tie, and tugged at his waistcoat. "I guess that concludes the business side of things," he said, stretching a hand across his long, precisely organized, mahogany desk. "Welcome to Torchwood Three, P.C. Gwen Cooper."

The attractive, brunette Welshwoman produced a gap-toothed smile and shook his hand firmly. "Thanks, Mr. Jones. I can't tell you how excited I am to be here," she said, looking around Ianto's neat office in Torchwood's vast underground base, commonly referred to as 'The Hub.'

"Ianto, please," he said, releasing her hand and sliding his own casually into his trouser pocket. "We're a bit informal around here."

"Ianto, then." She grinned again, casting her eye appraisingly over the tall, svelte, handsome young man in a flawless three-piece suit, whose blue eyes and dark, neatly styled hair contrasted appealingly with his pale, Welsh skin.

"Well, let me introduce you to the others," he said, stepping out from behind his desk and pushing open the door of his office.

Gwen followed him as he approached a pretty, petite Asian woman who was bent over a piece of electronic equipment, a light shining on her straight, glossy, black hair. "Gwen Cooper, meet Toshiko Sato, our resident computer genius."

Tosh glanced up briefly. "Hello," Gwen said with a friendly smile, proffering her hand.

"Mmm," Tosh murmured, eyeing her skeptically before pushing her fashionable glasses back up her nose with a finger, and returning her attention to her work. "This is Suzie's replacement?" she asked resentfully.

Gwen's withdrew her hand, looking doubtfully from Tosh to Ianto. "Tosh?" Ianto's tone held a warning note in it.

Tosh threw down her minuscule screwdriver with a sigh and stuck out her hand. "Welcome," she said with a forced smile.

Gwen took her hand. Tosh gave it one firm shake before dropping it as though it had burned her. Gwen frowned, wondering what the hell she had walked into.

Ianto nodded briefly at Tosh, then lead Gwen to a sunken medical bay. A young man with light brown, strategically messy hair, and wearing a white lab coat, on which several gaudy pins adorned the lapels, was using a device Gwen had never seen before to slice out organs from the monster she had helped Ianto kill just the day before. A Weevil, she reminded herself. It's called a Weevil, and it's an alien. From another planet. These people fight aliens… And I'm going to be one of them. She couldn't help smiling again as a thrill of excitement coursed through her and sent her spine tingling. Aliens… I'm going to fight bloody aliens, she kept repeating over and over again to herself, trying to wrap her mind around the startling bit of knowledge.

Ianto descended the steps and Gwen followed, grimacing at the sight of the eviscerated creature on the metal table. She averted her eyes, looking instead at the man in the white coat. He's a bit nice, in a roguish kind of way, she decided. "Gwen Cooper, this is Owen Harper," Ianto announced in his precise phonation.

"Doctor," Owen corrected coldly. "Doctor Owen Harper."

Ianto nodded. "Doctor Owen Harper takes care of all of the alien autopsies and sees to our medical needs." He had emphasized the word 'doctor.'

Gwen looked at the doctor's slime covered latex gloves and decided she could forgo the requisite handshake. "Suzie's replacement?" Owen asked with a hint of spite.

Gwen glanced at Ianto, who was glaring at Owen with disapproval. "Well, welcome to Torchwood all the same," Owen said, before turning his attention back to the Weevil on the table. "Wonder how long this one will last," he muttered under his breath.

"Excuse me?" Gwen asked at the same time Ianto said, "Owen!" with obvious admonishment.

Owen shrugged, but didn't look up again from his work. Gwen looked at Ianto. He had told her that they had a job opening at Torchwood, but he hadn't explained the circumstances behind that opening. Once again she wondered what she had gotten herself into by agreeing to join this unusual, eclectic team.

An alarm sounded, startling Gwen into an involuntary jolt. The Hub's main entrance, a massive door in the shape of a cogwheel, made a loud grating sound as the gears ground together and it rolled open. Gwen glanced again at Ianto, who rolled his eyes and looked conspicuously annoyed. "Hey kids!" a booming voice with a distinct American accent filled the space. "I'm home. Did ya miss me?"

With a sigh, Ianto ascended the stairs to the main work area. Gwen followed curiously, her eyes landing on a tall, well-developed man with underwear-model good looks; piercing blue eyes, chiseled features, and fashionably gelled brown hair. He was wearing a 1940's military-style grey greatcoat and standing with his legs spread wide and his arms crossed over his chest. The whole room seemed to vibrate with his presence. "Well, well, well," the man said, eyeing Gwen lecherously. "What have we here?" He practically licked his lips.

Gwen stared open-mouthed. The man absolutely radiated sex. She cleared her throat and swallowed hard.

"Gwen Cooper, meet…"

"Captain Jack Harkness," the man interrupted Ianto, sticking out a hand. Gwen took it, and felt a tingle run through her fingers and up her arm at his touch. She shuddered. "New recruit?" he asked Ianto.

Ianto nodded. "Harkness is our freelancer," he said in a constrained voice.

"And so much more," Jack said, insinuation oozing from every syllable.

"You won't see much of him," Ianto added quickly.

"Well," Jack smiled a leading-man grin, his straight, even teeth nearly glowing white. "Now that we have such a knockout traipsing around the Hub…"

Gwen felt herself blushing furiously and lowered her eyes coyly. Who is this man?

"Ianto," Jack said, his eyes casting the same lecherous appraisal over Ianto that he'd bestowed on Gwen. "Looking delectable as always. Love the suit!" He grinned cheekily.

Gwen raised a curious eyebrow at Jack's obvious wide range of sexual appetites.

"Jack." Ianto was literally biting back rage. "I won't tell you again about insubordination and sexual harassment in the workplace. If I could fire you…"

"I know. I know." Jack's face retained its brazen expression. "You'd kick my ass out the door in a heartbeat. But who would do all of your dirty work, hmm? Who's the one that realized Suzie…"

"Jack!" Ianto cut him off with a look that caused Gwen's toes to curl in her stylish, yet practical boots.

Remind me not to get on Ianto's bad side, she thought, staring with something like awe at her new boss. "My office! Now, Jack!" Ianto said in a seething tone.

Jack stood to attention and saluted, winking mischievously at Gwen, who bit her lip to maintain a serious expression. "Toshiko, show Gwen around, please," Ianto ordered as he turned on his heel and walked determinedly towards his office.

"He's a bit scary, no?" Gwen whispered to Jack.

"You have no idea, princess!" Jack replied before following their boss into the inner sanctum.

Ianto sat down stiffly behind his desk. He pushed the large calendar a centimeter to the left with his index finger, then neatly rearranged the pens that were already precisely lined up. He took a deep breath, trying to stifle his rage.

Jack sauntered in a moment later, threw his muscular frame into the chair opposite, leaned back, and put his feet up on Ianto's desk. With an angry scowl, Ianto reached across and shoved Jack's feet unceremoniously. They landed on the floor with a loud thump. Jack grinned at him maliciously. "You know, Jones, you really need to get laid," he commented, clasping his hands behind his head and tipping the chair back on its hind legs.

"Harkness!" Ianto roared. "We've had this conversation before, and I don't want to have it again! I just barely tolerate your presence here because…"

"Because of my unique condition, which makes me a valuable asset for the dangers faced by Torchwood operatives," Jack recited, having heard the speech a hundred times before. He looked at Ianto disdainfully. "I can't die, so I'm useful to you. Plus I've been around longer than any of you have been alive. But you can't stand me. You think I'm obnoxious, insubordinate, untrustworthy, and unpredictable. You've said it all before, Jones. Get some new material."

Ianto clenched his fists, his face turning several shades of crimson. His indignation and outrage were palpable, and for a moment, Jack almost quailed under the hatred in the other man's gaze. Then he shrugged nonchalantly. My time here is almost over. As soon as the Doctor comes, I'm outta here. And it can't happen a minute too soon. He looked scornfully at his 'boss.' Of all the self-important, finicky, stuck-up, humorless, cold-blooded bastards, I have to get stuck with this guy. At least Alex had a soul…

"Harkness," Ianto began in an exaggeratedly controlled voice. "You're useful to Torchwood, yes. But we all have our limits, and the world will keep spinning just fine without you. Either you show me some respect, or I'll have you out on your arse."

"What would Torchwood London say about that?" Jack asked looking unbearably smug.

Ianto was so desperate to slap the arrogant look off Jack's face, he had to grip his chair to restrain himself. "I don't give a damn what Torchwood London would say about that. I'm the leader of Torchwood Cardiff. I don't answer to London."

"You just keep telling yourself that, Jones," Jack said snidely, leaning forward and propping his elbows on Ianto's desk. "What's it been now, six months since you took over? And you're still calling London every five minutes. Can't seem to maintain a full team, huh? And I'm sure Hartman wants daily reports on little old me." He grinned and flamboyantly batted his eyelashes.

With a concerted effort, Ianto forced himself to ignore Jack's taunting remarks and maintain his professional demeanor. "The others don't know the facts about Suzie, and I'd like to keep it that way."

"Whatever," Jack said indifferently. "You're the boss," he added with obvious venom. He pushed back his chair with a blood-curdling scrape that caused Ianto to wince. "We done here?"

"We're done. Now get the hell out of my Hub. I'll call you if I need you. Hopefully later, rather than sooner."

"Sir, yes sir!" Jack saluted ostentatiously, then turned and sauntered out of Ianto's office, slamming the door behind him.

"Wanker!" Ianto spat as soon as he was alone again.

He put his elbows on his desk and rubbed his hands over his face. At least he had a complete team once again. He hoped this time they would last.

He sighed wearily and looked around his tidy office. He was fully aware of the fact that he'd been sent to lead Torchwood Three as punishment. It was a job that no one wanted. He knew - everyone at Torchwood London knew - that it was his fault Lisa had died.

Lisa… His eyes burned, and his stomach roiled as though it were full of rats, as it always did when he thought about his dead girlfriend. Lisa… He had loved her desperately. We were going to get married, leave Torchwood and all of the insanity behind… start a family… Now she's gone forever, and it's all my fault… And I'm stuck in this dump.

He groaned audibly, and thought for what seemed like the hundredth time about leaving Torchwood for good. But where would I go? What would I do? There's nothing for me out there in the real world… No family, no friends… Besides, my life expectancy is greatly diminished in this job... Less time I'll have to endure this pain…

Mustering all of his strength, Ianto pulled himself together and wiped furiously at his moist eyelashes. He was a leader now. He couldn't show any signs of weakness. It would never do.

Once again he straightened his calendar, realigned his pens, picked up the heap of files and knocked them against the desk, letting them fall into an orderly stack, before carefully placing them down again.

He rose from his chair, adjusted his tie, pulled at his waistcoat, and fastened the top button of his suit. Then he stood up straight, threw back his shoulders, relaxed his features into an expressionless mask, and strode confidently out of his office.