The Time Traveller's Son

Author: Milady Dragon

Disclaimer: I don't own anything here, except for my own, really strange, imagination.

Author's Note: I have discovered that there are more stories that I haven't posted here yet, and this is one of them. Please don't ask me where this came from...I blame the nachos.

The silvery, futuristic gun would have been intimidating if it wasn't for the woman holding it looking that much more terrifying.

"I want my son," she growled, as she pressed the muzzle of the gun into Nick Fury's eye patch. "I want my son and I want him now."

Fury wasn't one to bend to anyone's demands, but at the same time he knew River Song; knew she was perfectly capable of blowing his head off and not thinking twice about it. She was almost on a level of Natasha Romanoff scary, which was saying something, but it wasn't anything that Fury hadn't dealt with in the past and could deal with again.

The man, though…the man leaning nonchalantly against the wall behind her was another matter entirely. He might have looked far too young and really silly in that long purple coat, but Fury knew just how deceptive that façade was.

"Did you think we wouldn't find out, Director Fury?" the man asked, sounding almost bored. His pale eyes told a different story entirely.

Fury held up his hands, making the move slowly, trying to placate the pair that was currently threatening him in his own office. "I would have contacted you if I'd known how –"

"We heard about it from Clint," River snarled. "And that was only after we'd been trying to reach Phillip for weeks. We had to hear it from his traumatised friend!"

Fury hid his wince. Alright, so waiting so long that Barton had to break the news had been a bad idea, but this accusation was just bullshit. "It's not like I have the TARDIS on goddamned speed dial!"

"Now see," the Doctor said – and yes, this was the legendary Time Lord – said, "that's what I have trouble believing. Phillip would have given you a way to contact us in case of emergency."

Fury wasn't about to admit to having that information. What he'd done…well, he'd done it to bring his friend back, and he'd have done it all over again in a heartbeat. He'd known at the time that Coulson's parents would object; hell, if Coulson ever found out the complete truth there would be hell to pay. It still didn't make Fury backpedal though; Phil Coulson was a good man, and one of the very few people on this planet that Nick Fury trusted. There was no way he was gonna let him go without a fight, even if it meant facing the Doctor and River Song over some sort of crazy-ass laser gun.

"This doesn't answer my original demand," River Song cut in. "I want my son. I know that you must have him. We want to lay him to rest somewhere not on Earth."

The pressure from the gun increased, and Fury tilted his head back just a bit in order to relieve it. Under River's anger was grief; horrible grief that should have made him feel guilty about hiding things from the two of them but really didn't. Phil's slightly alien physiology was one of the reasons he'd risked using the TAHITI protocol on him, besides the fact that Coulson was his damned friend. "I'm sorry, but I don't have him anymore." Which was the truth; Coulson and his team were somewhere in Italy, tracking down Ian Quinn.

The Doctor stiffened. He might have resembled some awkward idiot in weird clothes but there really wasn't anyone more dangerous currently on the Helicarrier...hell, on the entire planet. He would have paid good money to see the Doctor face down Loki, because that damned mad god wouldn't have stood a chance. "And just what did you do?" he asked, his question deceptively soft.

Nick Fury wasn't stupid, by any stretch of the imagination. He knew that pissing these two off – well, more than he'd already done – would be disastrous. He wasn't about to test their patience when it had to do with their only child.

So, he told them exactly where Coulson was.

Not what he'd done to bring him back, of course. Although Fury knew if Coulson ever really remembered what had happened there would be no stopping the Doctor and River Song from coming back and dropping his ass into the nearest black hole.

"Wait," River said, giving him the side-eye while pulling her weapon away from Fury's face, "you're saying Phillip is alive?"

He barely contained the eye roll. "Yeah, that's what I'm saying. He's just fine." Well, he was, according to Melinda May.

"Then why do Clint and Natasha think he's dead?" the Doctor wanted to know.

"Because they aren't cleared to know the truth."

"I really don't think that's a good enough reason to keep this from two of the people he's closest to on Earth," River accused. The gun was back in its holster, but her hand was resting on the butt of it just in case she'd need to redraw.

"Let alone his parents," the Doctor pointed out.

"There was a time when our doctors didn't think he'd pull through," Fury said, keeping to as much of the truth as possible. "Loki's spear had done a shitload of damage and there wasn't any sign of him regenerating. Also, his 'death' motivated the Avengers into saving the planet. Keeping Coulson dead was the best thing to do under the circumstances. And sorry if I didn't know how to contact you. You can bring that up with Phil when you see him." He really was counting on them being so glad to see Coulson that the subject wouldn't be brought up.

Fury watched as River Song and the Doctor looked at each other, having one of those silent conversations that only spouses and covert agents can have. He knew he was playing a dangerous game, because with those two he couldn't depend on them not being able to find out in some way that Fury hadn't taken into consideration. Hell, who knew what freaky powers the Time Lords had?

Of course he'd known he wouldn't be able to get away with hiding Coulson away, but Fury'd hoped it would have taken them just a bit more time to find out. So much for that.

Finally, the Doctor turned back to him, the look in his eyes giving Fury an idea of just why he was called the Oncoming Storm. "Tell us where he is exactly. And if we find out there's more to this story than what you've said…" He leaned over the desk, pinning Fury with that thousand-year stare that had even Daleks shitting their shells, "you won't want to know what will happen."

"Of course he does," River added, her smile like a knife. "He wants to know so he thinks he can prepare for it."

The Doctor didn't say anything. He really didn't have to.

Fury watched them leave, not even bothering to wonder how they'd gotten on board the Helicarrier anyway. It didn't matter. What did was that now they knew, and Fury knew it was just a matter of time before his actions would come back to haunt him.

Still, he'd do it all over again. And he knew they'd just be glad to get their son back, because parents were like that.

Several months later, SHIELD fell.

It occurred to Fury as the three helicarriers were busily crashing into the Potomac, that the Doctor could very well have known about HYDRA. That this was some sort of punishment for how he'd brought Coulson back.

Then he dismissed it, because while he was well aware that the Doctor could topple governments – hello, Harriet Jones – that he'd never let innocent people get hurt. Of course, that didn't let Fury off the hook, but playing dead was always a good option.

Yeah, that should work.

Skye was the one who heard the strange noise coming from one of the storage rooms in the Playground.

She immediately forgot the errand that had sent her there, wishing she'd brought her gun with her. Still, she opened the door to the storage room and stepped in, putting her back to one of the shelves and searching for the source of that crazy sound, because she was an agent of SHIELD and curious as a cat when faced with plastic grocery bags.

She didn't hear it again, but she most certainly heard the man and woman arguing.

"Are you sure you've got it right this time?" the woman snarked.

"I don't question your abilities to navigate the TARDIS," the man exclaimed hotly.

"That's because I actually know how to fly her," the woman said back, and Skye thought she sounded fond.

The pair came around the corner just as Skye ducked behind her shelf. From the glance she got, the woman had wildly curly blonde hair, dressed like something out of a pirate movie only with a futuristic-looking gun in a holster at her waist instead of a sword. The man was tall and gangly, his long coat had a purple cast to the fabric and his pants were too short. And yet, somehow, it suited him.

"It's not my fault the old girl didn't want to arrive so soon," the man argued on. "I can't help it if she was being stubborn."

They walked on, and were past Skye's hiding place before the man spun in place, and she was struck by just how old his eyes appeared. He examined her for a second, just like he was peering into her soul, and then he gave her a friendly smile. "Hello," he greeted. "I'm the Doctor and this is River Song."

There was just something about him that made Skye open her mouth and answer back, "I'm Skye." Then her brain seemed to get back into gear. "Just how did you get in here, anyway?"

"Oh," he waved his arms, "we're just good that way!"

River Song rolled her eyes affectionately. "You have to excuse him; he can be a bit dramatic."

"Me?" the Doctor exclaimed. "I don't know what you mean." He turned back to Skye, who was beginning to feel like she was trying to deal with something that was way over her head…and she wasn't given to rampant stupidity. "We came by TARDIS, of course! We'll let you meet her later, but right now we're looking for Phillip Coulson. Would you mind taking us to him?"

Skye knew these two strangers were trouble. It wasn't just her being paranoid, either. The pair might seem harmless but there was something about them that she couldn't put her finger on. They both stood there, giving her these innocent expressions that she just didn't trust for a second.

And yet, she really didn't have a choice. She was unarmed, and she'd been around Melinda May long enough to know just how dangerous people could be even when they seemed like a couple of harmless crackpots.

Well, harmless crackpots who were visibly armed.

Besides, if she got them out of the storage room, the internal security cameras would pick them up and she was certain that someone would be out to meet them just as soon as Koenig noticed.

So Skye pushed past them to the closed door. Opening it, she asked, "Just how do you know Coulson, anyway?" She hoped they would give her some sort of clue as to what was going on, and if she was gonna have to throw herself into danger in order to save her boss from death…or worse.

The Doctor waved her through, and then looked at River and said, "Ladies' first."

River gave him a brilliant smile and took the invitation. "Thank you, Sweetie."

Skye led them down the corridor, toward the main areas of the Playground. Neither one had answered her question about how they knew AC – she'd tried calling him DC, but it just didn't have the same coolness factor – and she was about to ask once more when the Doctor piped up, "This looks like some sort of World War Two facility." He was looking around almost excitedly. "I've lost track of how many times I've been in World War Two…"

"Say what?" Skye blurted, torn between wanting to know and wanting to step away from the crazy.

"Spoilers," River remonstrated calmly.

"Oh yeah, right."

"Hold it right there!"

And there was the Cavalry. Skye felt pretty safe calling May that in her head, because she didn't think anyone but Coulson could read her mind with any accuracy.

Melinda May stepped out into the corridor from the junction down the hall, an ICER in her hand. Tripp was with her, and in his arms was one of the ginormous big guns he seemed to like really well.

Letting her survival instincts finally kick in, Skye bolted down the corridor, only stopping when she was next to Tripp. He smiled at her as she took a step back and let him cover her; after all, she didn't have a gun and she really didn't want to be in the line of fire without being able to defend herself.

She might have lousy taste in boyfriends, but she did have some common sense.

The moment she'd turned back toward the two strangers though, Skye was tempted to shake her head at the sheer chutzpah of the pair. They simply stood there; River with a sly grin and the Doctor looking very pleased. "Melinda May!" he greeted. "We should have known you'd be here!"

Skye watched as May rolled her eyes and holstered her ICER. "What are you two doing here?" she asked, and for a second Skye wondered if she'd been dumped into some sort of alternate universe because the older woman sounded fond.

"We've just found out about Phillip," the Doctor answered. "Well, maybe not just…more like a while back but the TARDIS seemed to not want to show up until now…where are we, anyway?"

"It's called the Playground," May answered. "It's a decommissioned SHIELD base from back before it was even SHIELD."

"The SSR?" the Doctor looked excited, his feet moving as if he was dancing, and not doing it very well at all. "I once met Peggy Carter, you know? Lovely woman…knew how to make a spectacular cup of tea…"

The guy was a name dropper, too? For some reason that didn't surprise Skye, even if she'd just met him.

And it really just reinforced how crazy she thought he was.

The sound of running footsteps had Skye looking across the hallway junction, and she couldn't help but smile as she saw Coulson barrelling down the corridor, followed closely by Fitz, Simmons, and Koenig. She couldn't help but feel relieved. Coulson would handle things. He'd save them all from the weirdness that was currently taking place before Skye's eyes…

Coulson came to a halt, staring at the strangers, an expression on his face she couldn't identify. "Mom? Dad?"

Say what?

The woman, River, completely ignored the huge gun Tripp was still aiming in her direction to dart forward, wrapping her arms around Coulson like she was some sort of two-tentacled octopus. "Oh, my baby," she exclaimed.

Skye couldn't see her boss's face, but from the sudden slump of his shoulders she knew the moment he decided to crumple under the weight of motherhood's caring embrace.

She didn't know whether she was shocked or disappointed.

River pulled back a little, looking at Coulson like she could see into his head. "What did that man do to you?" she growled, and in that moment Skye learned what a mama bear would sound like if someone had injured her only cub.

"Mom, I'm fine…"

The Doctor also came forward, and in his hand he held a silver tube-like thing. He shook it once, and the end opened, revealing a green light. "You could have called us, you know."

"Your father's right," River chided. "We had to find out from Clint, that poor young man. He was practically blaming himself for getting you killed…"

Coulson flinched at that, and Skye wondered just who this Clint person was, because he was obviously someone important to her boss.

"I am sorry," he answered. "But I thought for sure Fury would call and say something…when you didn't show up immediately, I thought he had."

"I knew he had our number!" the Doctor crowed. "I'm going to need to have serious conversation with that man."

"You really should call Clint and Natasha," River said. "They deserve to know, like Melinda here. She's known all along, I would assume."

"Not all along," May corrected. "I was told Phil was dead just like everyone else. I found out later."

Skye decided that she'd take her cues from May, and since the older agent wasn't moving to take that device away, and in fact seemed perfectly relaxed with what was going on. Skye figured it must be all right since May was all about bodyguarding Coulson. In fact, May was looking smug, like she knew something they didn't –

Oh, yeah.

The tube began to hum, which prompted the Doctor to wave it all over Coulson like some sort of bizarre flashlight.

"Wait," Fitz exclaimed.

"Just what is that thing?" Simmons asked practically over his question.

"The sonic?" the Doctor clarified. Then he blew a raspberry at them. "It's nothing."

"It does come in handy when you want to build shelves," Coulson said wryly. "I still recall trying to use it to open a jar of pickles."

"The jar exploded all over the kitchen," River laughed fondly. "It was just so cute."

"You only think it's cute because you didn't have to clean it up," Coulson snorted.

"Of course, darling!"

Oh god, this was actually adorable. Skye hoped that Koenig was recording all of this, and if not, why wasn't he?

"Sonic what?" Fitz asked, his science face clearly in place as he kept his eyes on the glowing stick of sonic whatever. He was practically drooling.

"Aren't you adorable," River cooed. "Phillip, won't you introduce us to your friends?"

Skye caught the eye roll her boss gave. "They're my team, Mom."

"Doesn't mean they can't be friends!"

Coulson acknowledged her point with a nod and a small smile. He went around the hall, starting with, "You know Agent May," and ending with, "and these are my parents, Professor River Song and the Doctor."

Simmons suddenly began bouncing up and down. "The Doctor? The Time Lord Doctor? The Time Lord Doctor who worked for UNIT?" She was actually squeaking.

Skye was so going to pin Simmons down and get some answers out of her, even if she had to tickle her to do it…it just wasn't fair that she knew and no one had even bothered to explain much to Skye, herself, yet.

The Doctor stopped what he was doing in order to stare at Simmons. "You seem to know a lot about me, Agent Simmons."

Simmons nodded enthusiastically. "My Uncle John was with UNIT in the seventies…" then she frowned, "or was that the eighties…?" She shook her head. "Never mind. My uncle is John Benton."

The smile that the Doctor displayed was so bright Skye wanted to reach for a pair of sunglasses. "Sergeant Benton? He's a good man; really knows how to blow things up."

Simmons practically radiated pride.

Skye wondered if this uncle was where her scientist friend had gotten her love for explosions.

"Wait," Fitz said, finally looking away from the shiny silver thing, "this is the Doctor you talked about? The one who travels in time?"

"Yes, exactly!" Simmons gushed like a teen with a celebrity crush.

"He's a time traveller?" Skye finally decided that the wait for answers was over.

"Oh yes," Simmons confirmed. "I can tell you stories –"

"Let's not for right now," May interrupted. Skye hadn't even seen her approach, which was par for the course for SHIELD's resident ninja. Sometimes Skye wondered who got that from whom: if May had taught Coulson, or if their boss had shared his secrets of sneakiness.

"This isn't good," the Doctor muttered just loud enough to get everyone's attention. He was still staring at his sonic whosits, but at least he wasn't waving it at AC anymore.

Although Skye kinda wished he was because he didn't look happy at all.

"What is it?" River asked, concerned.

The Doctor snapped his thingy closed, and his face was the very picture of pissed off. "Whatever it was Fury used to bring you back has blocked the regenerative energy that would have normally brought you back on its own."

"Wait," Coulson said, frowning. "I thought regeneration wasn't going to happen, because I'd been born with a nearly human physiology…"

"Now you're saying you're alien?" This had passed beyond the realm of crazy and into Skye's outrageous imagination. She wondered if she was really asleep.

"My dad is an alien," Coulson confessed as if the knowledge had been dragged out of him. "Mom's closer to human."

"You're an 0-8-4!" Skye exclaimed. No wonder he'd known that there were worse things than knowing the truth. Coulson might have gone through the same thing at some point!

She suddenly felt much closer to her boss than she ever had before.

"I really do hate SHIELD's little categories," River scoffed.

"Can we get back to what I was saying?" the Doctor called out. He paused for effect, and then went on, "Thank you. Now, yes…I was certain regeneration was out of the question. But something must have affected your biodata, because there's a very large build-up of regenerative energy and it needs to be either bled off or let run its course."

Coulson pinched his nose like he did when he was getting a headache. "And I suppose this needs to be done now?"

"Better now than later," the Doctor agreed. "C'mon, we can do it in the TARDIS. And you can explain to us exactly what Fury did in order to bring you back to life."

River linked her arm with Coulson's. "We still have your room all ready," she said, beginning to drag him back toward the storage room.

Skye couldn't help but grin at the irritated yet fond expression on Coulson's face. "I'm sure you do."

This she had to see.

Apparently, so did everyone else, because the entire team followed the Doctor, Coulson, and River Song like a straggling line of puppies. River was speaking to Coulson softly, and no matter how close she got Skye couldn't overhear what they were saying. Still, she had enough to think about; her boss, her AC, was an honest to God alien and now her brain was gonna start dribbling out of her ears because it was the very last thing in the world she'd ever have expected.

The TARDIS was something else, too.

Skye might have been a bit disappointed by the big blue box if it hadn't been for Fitz. "This is the model you got me for my twentieth birthday!" he squealed, hugging Simmons and practically choking her.

Oh yeah…she'd seen it in Fitz's quarters on the Bus. Skye had wondered what it was at the time she'd noticed it but it had slipped her mind.

"You have a model of my TARDIS?" the Doctor asked, grinning manically. "Oh, she'll like that."

"My uncle made it," Simmons answered happily.

"Simmons gave it to me when she started telling me stories about you," Fitz finished excitedly.

"Then you really must come in and meet her officially." The Doctor took a key from his pocket. He fit it into the lock in one of the two doors, and then flung both open as if he was performing an especially good magic trick.

Skye had to admit, looking into the inside of what was a box on the outside and a spaceship on the inside, that it was a particularly good trick.

Not for the first time did she think that AC was the coolest person in the world.