So, aliens visited Earth and the first people they came to were the Avengers. Something to do with a warrior culture that valued heroes over policy makers. Tony could get behind that, mostly because he was more interested in getting his hands on whatever technology the youngest alien was happily calling "magic" than in... making sense.
According to Thor and Loki, princes of the realm eternal, the universe was a big place full of tree metaphors and realms, and it was time for Earth to take its place on the bigger stage. Somehow in conversation of that bigger stage, the subject came up of the Second Prince's Father. Like it was a funny story to tell newcomers. Apparently nobody knew who he was.
"Well, Laufey's not telling, and enough people have come forward with a claim that it's essentially a farce. It could be Odin," Loki said, rolling his (startlingly green, Tony couldn't look away) eyes. "It could just as easily be Oberon of the Ljosalfar, or Glut of Muspelheim. It's practically a badge of honour among the elder races to have a candidate. I've been of age for a thousand years. There are galactic laws -- there's lore dictating how much favour I'm allowed to show each of my fathers. One of the sillinesses inherent to interstellar politics, really."
And that was cool. But somehow in there, Tony caught a flavour he was used to. Paternity unknown. And for the first time in twenty years or so he flipped his usual reaction to that. He wanted in this race.
And he totally never knew when to shut his mouth.
"What?" asked Tony at the staring faces of his team mates. "I could be. Do you know how many paternity suits I get a year?"
"What is a paternity--" began Thor, while Steve rolled his eyes.
"Stark, I knew your father," he said in that way he had that was calculated to annoy. Tony hoped he would grow out of that soon, before he had to punch the guy. "I know you're not secretly a thousand years old."
"Stark Industries has been working on Time travel for a couple years now," he said without hesitation. It could be true. They didn't know. "I'm pretty sure we're on the edge of a breakthrough. First destination planned was the planet, uh--"
"Jotunheim," supplied Loki without looking up. He was sitting with his head in his hands, shoulders quaking with silent laughter.
"Planet Jotunheim! A thousand years ago. You know, these things happen." He shrugged, looking suitably contrite.
"I'm pretty sure they don't," offered Bruce. Tony ignored him.
"It was a whirlwind romance! Or, I'm sure it will be. Time travel. I'm getting my tenses in a twist."
"...Father?" asked Loki in a small voice. Tony looked over. Loki had wiped the smile off his face, and was looking up at him with childlike wonder. "Father, is it truly you? I've been hurt before, Father, please say it's real this time!"
Tony kept a straight face with a heroic effort. "Yes, kid. It's real." He opened his arms, and Loki came to them unhesitantly. "Come give your old Dad a hug."
Loki did. "Oh, Daddy, finally!"
"Brother," said Thor in a voice of fond exasperation. "Brother, this mortal is not actually your fa--"
"Don't be dense, Thor, of course he is. Look at the two of us!" He pulled Tony around to present the both of them to his brother. "We look exactly alike! That can't be a coincidence." Tony glanced up at what had to be nearly a foot of height difference, and the long features, bright green eyes and the plethora of genetic markers... They both had black hair, so that was something. "No, Thor, it must be true. Oh, Father, I'm so glad I've found you at last!"
He threw both arms around Tony's neck as Thor snorted amusement. Tony reeled to bear the extra weight. "Hey, that's my boy," he muttered in the most paternal voice he could manage. "Hug it out, now."
"Oh, for the love of..." Behind them, Steve was looking more disapproving with every second. "Natasha, you're his friend - can't you talk sense into him?"
"I tried for two months as his PA, that didn't work." Natasha wasn't even trying to hide the laughter in her voice. "What about you, Thor?"
"I have been Loki's brother for near a millennium, Lady Widow. If it has not worked thus far, I feel it never will." Hanging around Tony's neck like an unwieldy necklace, Loki was shaking with suppressed laughter again. He maintained the hug like a champion, though.
"Look on the bright side, Cap!" said Clint. "We're all uncles!"
"Oh, my god," said Bruce. "Who's going to tell Pepper she's a stepmother?"
"A God's stepmother," corrected Natasha. "I think it should be me."
"No way!" Tony protested. "I should tell her myself, it's only fair!" I came up with this one, I want to see that little quirk her lips do when I've actually surprised her. He started to make for the door, to get Pepper on the phone when he realised his movements were being a little hampered by his new godly son still clinging to him. Loki had his eyes closed, a blissful little smile on his face.
"You, uh-- You gonna let go?" he asked.
"No," Loki said happily. He snuggled a little deeper into the juncture of Tony's shoulder.
Thor went back to Asgard to break the news to their father, while Loki cheerfully moved in to Stark Tower. Tony wondered briefly if he was in over his head, but he wouldn't be Tony Stark if he let that thought bother him. Besides, Thor mentioned to Fury before he left that the plan had been for Asgard to leave at least one ambassador behind all along. So it was better for everyone to just let it happen, and experiment on Loki's magic as far as Loki would allow it.
Pepper dealt with the whole situation quite well actually. When Mothers' Day rolled around, Loki gave her a card made of macaroni and a kiss on the cheek. And a bottle of perfume that he claimed had come from an elf-market in someplace called Nornheim. It made her smell like an angel.
In fairness, Loki didn't spend all his time on Tony's couch. He just pretended to. The time not spent casting magic spells in full body scanners was taken up with his ambassadorial duties, which he apparently took seriously or something. Tony wasn't paying attention.
He paid attention when SHIELD started trying to lock Loki in (and it had nothing to do with the way they were trying to manipulate his kid). Coulson was hanging around more often, and Natasha casually moved her things into the Tower. It made Avengers business a hell of a lot easier, actually, so Tony went ahead and moved the rest of them in. Clint got the top floor. Bruce got the lowest residential floor.
Loki was obviously fascinated by their war stories - warrior culture, more value on heroes than politics - and tried unsuccessfully to hide that fact. SHIELD pounced on that opening.
"You know, there's still an open spot on the team, Mr Odinson," said Coulson, a few months into Loki's stay.
"Tonyson," said Loki.
"Mr Tonyson. I thought it was time." He threw a dazzling smile at Tony, who returned it around a mouthful of breakfast cereal. "Technically it ought to be Laufeyarson, but I don't know, I think Tonyson just sounds right. Loki Tonyson..."
Coulson hadn't closed his mouth yet. Tony paused in chewing.
"Oh!" said Loki, "Do you think I could get new stationary? From the desk of Loki Tonyson."
"Are you speechless?" asked Tony, delighted.
"No." Coulson shut his mouth immediately. "No, I'm not. But, ah, do you think it's smart to change your name in the middle of negotiations with--"
"Oh, you're right," said Loki in disappointment. "Fine, I'll keep Odinson."
"You were so speechless," grinned Tony.
A few weeks later it came out that about fifty per cent of the time Loki was in Tony's lab casting spells for him was actually a clone built out of magic, and not Loki at all. Tony grounded Loki, and took away his TV privileges. He was shocked that it worked, until he realised that of course the Loki sitting obediently at his desk was a clone. Loki was hiding out on Natasha's floor.
SHIELD (Coulson and Fury) roped Tony into helping recruit Loki to the Avengers. Neither of them said the words you're his father, talk to him. But they didn't say them pretty loudly.
Tony walked into the rec room on the 'public floor' of the tower, where everyone mostly congregated. Loki was on the couch, eating an orange and watching Clint murder Bruce at some racing game on the TV. "Hey," he said as he came in, "you're too old to be lying around playing video games. Get a job."
Loki blinked at him before remembering the game they were playing. He swung his legs up onto the back of the couch and sat upside down. "Got one," he said, through a mouthful of fruit. "I'm a lab rat." He stuck out his tongue.
"A real job. Don't you talk back to me, I'm your father--"
"--probably--" said Clint without looking away from the screen.
"--possibly--" said Bruce.
"--but not really," said Natasha from her seat in the corner. Steve was watching with a bemused smile.
"--I'm your father," said Tony firmly, "and I know what's best. That's it, you're joining the Avengers!"
A grin flashed across Loki's face before he replaced it with a pout. "But Daaad..."
"Not another word! It'll be good for you!"
Loki rolled backwards off the couch with a scowl. "Ugh, you're so unfair! Fine! I'll be a stupid Avenger!"
"Good." Tony dropped the stern Dad act, and jumped over Loki to steal his seat.
"I don't understand the future," said Steve softly.
"That's okay!" called Loki from the floor. "Neither do I!"
And so that was that. Loki said some things to some people, convinced a few world leaders that this in no way meant he was favouring the US since the Avengers were Earth's mightiest heroes. He asked Steve a couple of times how he felt about changing his name to Captain Midgard, and Steve grew a sense of humour long enough to ask Tony to control his son.
Loki finally caught on to how much he could unsettle Tony by calling JARVIS 'Brother'. Yeah, that was never going away. Especially not after JARVIS started returning the sentiment.
Loki started going out to emergencies with the Avengers. With the rest of the Avengers. He and Tony were occasionally (just occasionally!) a little overprotective of each other. Well, when you spent half the time being called Dad by someone, the paternal instinct tended to... creep.
Two months after Loki's recruitment, a paramedic was tending Tony for blood loss in the field, and asked Loki to donate for a transfusion. There were a few uncomfortable explanations as to why that was a bad idea. Then Steve turned out to be a universal donor and everyone pretended very hard that he had been the first option.
"Hey!" said Tony, trying to sound less drunk than he was. "Hey Romanoff! We gotta talk, we... what are your intentions towards my little boy?"
Natasha raised an eyebrow at the 'little boy' who towered over both of them. Loki affected embarrassment.
"Oh my god, Dad, I told you, we're just friends!"
"Yeah, your intentions better be honourable..."
Natasha hid a smile behind her own glass. "I don't think last night was the kind of thing that happens between 'just friends', Loki."
"It's not?" Loki blinked. He shook his head in disappointment. "Dad. You are a terrible role model." He threw a wink at Natasha and she rolled her eyes with a grin.
"Honourable!" shouted Tony again. "And-- with all the requisite protection!"
Loki chuckled. "Come on, Dad. I feel you should retire for the night. A little too far into your cup for polite company."
Tony put up some token resistance, but Loki scooped him up into a bridal carry. Natasha leaned over him for a quick kiss goodnight as Tony wondered muzzily if they hadn't got this 'bed time' thing the wrong way around.
Fathers' Day came around, inevitably. Clint circled the date on the calendar, and Steve bought a video camera and loudly claimed it was for other things. When asked, he couldn't think of any. Despite Natasha mouthing to him behind Tony's back. But when Sunday came Loki ignored him all day. Tony tried as hard as he could not to be disappointed. He would have liked a macaroni card of his own. Then after sundown, when there was no work left to do, Loki took him by the hand, dragged him into the lab and taught him the first magic spell he had ever learned. Tony summoned fire in his hand, and watched it dance until morning.
About a year and a half after first contact, and Earth was well along its way to having a universally accepted accord of all the things expected - announcements of non-hostility (as though anyone would try to wage war against Asgard), trade agreements (from each nation according to its resources, to each according to... how much cool stuff they just gave Asgard. Australia came off pretty well in the exotic pet trade. Apparently Asgard loved funnel spiders. England, too, just because they managed to claim Neil Gaiman before America thought to. The trade in stories had never been hotter than when the Norse Gods arrived.) Tony was not paying attention to those things, and so he was not thinking about how Loki's mission on Earth was almost over. Not even a little
Fury called him into his office. "I think we need to talk about the Loki situation."
Tony did not want to talk about the Loki situation. "There's a situation? Huh. You should probably ask Pepper about that stuff - she's the disciplinarian. I can just never get through to that kid--"
"Are you sleeping with him?"
Tony choked on his own tongue. "What?"
"I hate having to ask this twice, Stark, but - Are you sleeping with the alien ambassador?"
"I'm in a relationship with Pepper!" Tony said, because the first thing he thought was He's my son and he couldn't say that.
"And he's been sleeping with Agent Romanoff. But he's a Norse god with a reputation, and you're..."
Fury trailed off with an unsubtle look. "No!" said Tony. "No, Loki and I are not having sex."
One of Fury's yearly quota of smiles split his face. "Great. You never know with gods, but I don't want anything to disqualify us. Does Stark Industries actually have a time travel R and D project?"
"If not, I need you to start one."
"Director, I'm not actually Loki's--"
"I know," snapped Fury. "What do I look like to you, an idiot? But I've been talking to some people. Loki, Odin..."
So, it turned out there was some dissatisfaction up there about how much time Loki had been spending on Earth. Not just on Earth - with Tony.Some guy, Kvasir of Vanaheim had been complaining. He wasn't Loki's father either, but Loki hadn't been near him in decades and he was itching for his custodial weekend with the future advisor of the future king of Asgard.
"I'm, eh, not sure what this has to do with..."
"Stark, it means the other realms are taking your paternity claim seriously."
Tony stared. It was less staring than it was boggling, really. "Why?" he asked.
"It's never been about plausibility, Stark. Loki's Niflheim father is a zombie. Skeletal from the waist down. It's not about how credible the claim is, it's about how Loki reacts! Stark, how have you not noticed that you have a kingmaker crashing on your couch?"
"...I've been studying his magic tricks..." Tony felt faintly ill.
"Asgard controls the universe. Before too long, Loki's gonna control Asgard. At least, partially."
"...I sent him to his room last week."
"Don't do that again."
"I won't do that again."
It was decided that in the event of Tony's death then whoever inherited Stark Industries would inherit the position of "Loki's Midgard Dad". It was also decided that the decision as to who would inherit Stark Industries' R+D department, at least the Time Travel project, would no longer be Tony's to make. Since Tony apparently had no idea what he was doing when he claimed paternity in the first place.
Loki, when Tony confronted him, thought this was the funniest thing in nine realms. The rest of the team, when Loki gleefully told them, stared at Tony like they didn't understand how 'genius' could exist in a body with this much 'ditz'.
Finally there came the ceremony, all pomp and circumstance, of Loki leaving Midgard. Thor came to pick him up, and Kvasir was with him. Tony had no idea how he had managed that. He didn't pay attention to these things. It felt like a handing over of joint custody, with half the world leaders there to play social workers. Kvasir was blond, streaked with grey, and heavy. Tony looked at him standing next to willowy, dark Loki and couldn't help but snicker. "He looks nothing like you," he muttered out of the corner of his mouth.
Standing on a platform in front of representatives from at least three realms, Loki did not look at him like a crazy man. "You're right," he whispered back. "I should reject his paternity claim on that basis."
Tony suppressed the smirk. "We both have black hair. Obvious genetic match."
Loki turned a snort of laughter into a genteel cough, and Tony shut up until they were off the stage. At some point in the next few hours he found himself standing next to Loki and Kvasir again, shaking hands with Loki's Vanaheim Dad.
"How did you explain the discrepancy in your ages again?" Kvasir was asking him.
"Time travel," Tony said. He tried for a second to crush Kvasir's hand in his, then learned that apparently Vanir had the same super strength as Aesir. Jotnar, whatever. He extracted his hand quickly. "Now! You be careful with him. His bed time is ten, he can stay up til eleven thirty on weekends--"
"Oh, my god," muttered Loki. Kvasir looked deeply confused.
"And don't give him refined sugar, we haven't been letting him eat refined sugar, I don't know if it's been helping, you know how he can be--"
"Tony," said Loki. "Stop."
Tony did not stop.