AU Marvel Cinematic Universe

Thomas meets Tony Stark

Chapter One:

Anthony 'Tony' Stark, a self-proclaimed eccentric genius, billionaire, playboy and philanthropist. At four years old, he made his first circuit, when he was almost seven he built an engine. He graduated from MIT at the top of his class at seventeen. Then at the age of twenty-one, his parents were killed in a car crash and he inherited Stark Industries. At twenty-five, he found out he had a four year old daughter, Leanne, with a woman who died in a plane crash. Not long after, he had a house built on the cliffs of Malibu, with it's own A.I system named J.A.R.V.I.S.


The week leading up to the Christmas of '07, Tony was wrapping his daughter's present in his room when Pepper walked in. "Oh wow, I'll never get used to seeing this." she said, looking at Tony. He looked up with a slight smile. "Every year you say the same thing." said Tony, as he returned to wrapping. "You've been my Personal Assistant for ten years now. This is not strange."

"When you make me buy my own gifts, it is strange." said Pepper, looking at him. As J.A.R.V.I.S chimed in saying "Sir, your daughter has returned from the mall."

"Thanks J.A.R.V.I.S." said Tony, smiling. As he tucked Leanne's present underneath his bed. "Come on Peps, let's go greet our daughter."

"She's your daughter, Tony." said Pepper, looking at Tony, as the two of them walked out of the room.


Leanne took a seat on the sofa, leaving her bags on the floor by it. "J.A.R.V.I.S, TV please." she said, smiling. "Continue where I left off last night, please."

"Right away, Ms Stark." said J.A.R.V.I.S, as the TV turned on. She smiled, as she noticed Tony and Pepper standing at the doorway. "Pause it, J.A.R.V.I.S." she said, with a small sigh. As Pepper took a seat next to her. "Again?" asked Pepper, looking at her. Leanne smiled before saying "What can I say, I love the show." as she saw her dad walking over to the bags. "Oi, Dad, no peeking. You can wait a week can't ya."

"Oh you know your old man doesn't like surprises." said Tony, smirking, as he jumped over the back of the sofa. Leanne smiled and said "He's also terrible at keeping secrets, remember my eighth birthday. Mom set up that surprise party for me, but you let the cat out of the bag a week beforehand."

"Yeah, if I remember correctly you also told her what you got her over that same meal we had at that restaurant." said Pepper, looking at Tony. Before realizing what Leanne had said. "Wait, did you call me Mom?"

"I've been doing it for years." said Leanne, looking at Pepper. "Do you not want me to? Because I can stop..." Tony smirked, as Pepper shook her head. "You don't have to stop... we have known each other for a long time." As she finished, there was a crash outside. "Sir, it would appear there is an unidentified teenage boy outside with serious injuries. Should I call an ambulance?"

"Yes, straight away." said Tony, jumping up from the sofa. "Lea, stay here." He ran to the door, and flung it open. To see a teenage boy with brown hair stumbling towards it, in a black fleece, a black polo and black jogging pants.


Tony, Pepper and Leanne sat in the private room of the hospital the boy had been taken to. He was lay in the bed, unconscious. J.A.R.V.I.S was currently working to identify the boy, and then contacting whoever had guardianship over him. Until then, Tony felt a strange pull to make sure he's cared for. "Hey, Dad." said Leanne, looking at Tony. "Do you think we could take him in? You know, if he wants..."

"If he wants it, then yeah." said Tony, smiling. "I don't see why not." As he said that, the boy seemed to glow orange. When the glow disappeared, his wounds were gone and he was awake. "Where... where am I?" he asked, with a slight British accent. "Who are you?"

"I'm Tony Stark." said Tony, looking at the boy. "You were found on my driveway. You had some serious injuries..."

"Well, as you can see, I'm fine." said the boy, looking at him. "Although, I can't remember much... Should I know you?"

"Oh, this is gonna be fun." said Pepper, with a smile. "We've never met you. Do you remember your name?"

"I have some recollection of somebody calling me Thomas." he said, looking at her. Before noticing Leanne. "Well, hello there."

"Hey." said Leanne, with a slight blush. Pepper smiled slightly to herself before excusing her and Tony from the room.


An hour later, Thomas was being shown around the Stark house by Leanne. Tony and Pepper had to go into the Stark Industries main compound. "So, basically, this is home." said Leanne, concluding the tour in the front room. "You up for watching some telly?"

"Sure." said Thomas, smiling. Before noticing the Christmas tree and decorations. "Oh, it's coming up to Christmas?"

"This Sunday, yep." said Leanne, with a small smile. "I doubt we'll get snow though, it's too hot." Before taking a seat on the sofa. "J.A.R.V.I.S, put the Santa Clause on please."

"Right away, Miss Stark." said J.A.R.V.I.S, making Thomas look around. "Do you want me to start the Popcorn Machine?"

"Ooo, can't resist popcorn." said Leanne, smiling. She stood up, as Thomas said "I take it you know you're speaking to thin air... And that it's talking back..."

"Oh that's just J.A.R.V.I.S." said Leanne, looking at Thomas. "He's our A.I system. Dad created him when he built this house." She smiled, as she walked towards the kitchen. "I'll be right back. You can make yourself comfy."


A few hours later, Tony and Pepper returned to find Leanne and Thomas watching Christmas movies. "I thought we were gonna do this tonight?" said Tony, looking at Leanne. She looked at him and said "I was watching the same ones we watched last night." with a smirk. Tony smiled, before shaking his head. "I'll be in my workshop if you need me, OK?"

"Sure thing, Dad." said Leanne, smiling at him. As Pepper took a seat on the sofa. "So, what's next on the list?" she asked, smiling. "And what do you want for dinner? We should order in, I don't want to cook tonight. It's way too close to Christmas."


As dawn on Christmas Day came, Tony walked into the front room to find Thomas looking out the window. "Merry Christmas, Tommy boy." said Tony, looking at Thomas. Thomas turned to say "Merry Christmas, Mr Stark. You didn't need to let me stay, I could have found somewhere else to stay."

"A fifteen year old in LA, there's no way you'd be able to find a place to stay." said Tony, looking at him. "At least, not one where'd you be welcomed as nicely as here."

"This place is nice." said Thomas, with a smile. "I just feel like I should repay you. You barely know me and yet you let into your home. You've made me feel like... like I belong." As he said that, his face dropped and his eyes flashed with pain. "After what I experienced, I like the feeling of belonging somewhere."

"Well, you're free to stay here for as long as you want." said Tony, smiling. Before looking at his watch. "Hey J.A.R.V.I.S, wake up Leanne and Pepper would ya. It's Christmas!"

"Right away, Sir." said J.A.R.V.I.S, as Tony walked into the kitchen. "You up for some Christmas pancakes? Leanne loves them."

"I'll just have a drink." said Thomas, looking at him. "I don't really eat."

"We noticed." said Pepper, walking into the front room in her dressing gown. "But you have to try Tony's pancakes. They are divine. It's a shame he only makes them two times a year." Thomas let out a small smile before following Pepper into the kitchen.


Half an hour later, Leanne wandered into the kitchen. To find Thomas lent against the island while sipping a can of Pepsi, while Pepper tucked into a plate of pancakes. Tony finished plating up a plate for Leanne as she took a seat at the table. "Merry Christmas, princess." said Tony, smiling. Leanne planted a kiss on his cheek and said "Merry Christmas, Dad." before tucking into her pancakes. "Amazing, as usual. You HAVE to try some, Thomas."

"If I did, I wouldn't eat till tomorrow." said Thomas, smiling. "And I'm sure I'd feel left out if I didn't eat Christmas Dinner."

"Speaking of which, I need to put the Turkey in if we want Christmas Dinner at our usual time." said Pepper, smiling. "After that, we can open presents."


Ten minutes passed as Tony, Leanne and Thomas sat in the front room. Tony kept looking at the presents, while Leanne tried to stop him from opening them before Pepper joined them. Thomas took in the slight of the family in front of him, with a smile. He had never really had a family, before or after the war. But here, he actually felt wanted. "The turkey's in, now for presents." said Pepper, walking into the room. "Tony, do you want to open yours last?" Tony instantly stopped eying the presents. "Right, good. We'll start with Thomas."

"Oh no, you didn't need to get me anything..." said Thomas, looking at Pepper, as she picked up a present from under the tree. "I haven't got you anything."

"Oh please, tell me you wouldn't have felt left out." said Pepper, handing him the gift. "And you didn't need to get us anything." Thomas nodded, before taking the gift. He slowly unwrapped it, and smiled at the contents. It was a gray long-coat, made of wool. Pepper smiled and said "I hope it fits, Leanne picked it out."

"I thought it would look good on you... Better than that fleece, anyway." said Leanne, looking at Thomas. "But we are gonna have to go shopping, to get you something better than that polo and jogging pants."

"Hey they kept me alive. It was a war-zone, where I came from..." said Thomas, looking down at his clothes. Before shaking his head. "But you're right, I do need new clothes. Brighter ones." He looked at them and said "Thanks. This is the nicest thing anybody has done for me."

"No problem." said Pepper, smiling. "And now, Tony."


The next few hours were spent with Christmas movies on in the background while Pepper prepared the dinner. Tony was busy upgrading the R.C helicopter Pepper had got him, while Leanne was trying on the dress Pepper had brought her. Tom was keeping an eye on the news, as apparently a giant star had appeared above London. He slightly smiled, as J.A.R.V.I.S said "Sir, Colonel Rhodes, Mr Stane and his son are walking up the driveway."

"Open the door, J.A.R.V.I.S." said Pepper, walking into the front room. The front door swung open, and Thomas turned to see three people walking in with presents. "Merry Christmas, everybody." said Colonel Rhodes. "Is Tony here?"

"He'll be in the workshop." said Obadiah, looking around. Before settling on Thomas. "And who are you?"

"Thomas Potts." said Thomas, looking at Obadiah, with a smile. "I'm staying with Aunt Pepper till Dad gets back from wherever it is he's gone."

"Which knowing my brother will be years." said Pepper, looking at Obadiah. "Tommy will no doubt be here till he graduates from High School." Zeke Stane looked at Thomas, with disdain. Thomas just smirked. As Tony walked into the room with the RC Helicopter. "So, who wants to watch me fly this baby?" he said, looking around at the room, noticing the newcomers. "Oh hey guys. Merry Christmas."

"Merry Christmas." said Rhodey, smiling. As Obadiah said "Why don't us adults go get a drink from your bar, Tony. Leave the kids to talk." Obadiah walked into the kitchen, followed by Tony, Rhodey and Pepper. Leaving Leanne with Thomas and Zeke. Leanne stood up and said "I'll go and get us drinks." before walking out of the room. Thomas smiled as he watched her leave. Zeke scowled before saying "She's mine, Thomas."

"You wanna rephrase that?" asked Thomas, looking at Zeke. "Because I am not above violence. Understand me?"

"I'm not scared of you." said Zeke, looking Thomas in the eye. Thomas smirked and said "You barely know me. Course you're not scared of me. Yet." He stood up. "I'm gonna go help Leanne with the drinks."


As midnight came on Christmas Day, Thomas was sat in the front room. Tony had retired to his workshop, while Pepper and Leanne had both gone to bed. "J.A.R.V.I.S, can you check if there have been any unusual events in London over the last year." said Thomas, looking at the screen. "And show me any that have been followed by a sighting of a Police Box."

"Are you using my A.I to find your father?" asked Tony, walking up the stairs leading down to the workshop. "Because you could just ask him to actually find him."

"I'm keeping an eye on my old neighborhood." said Thomas, looking at Tony. "Is there anything wrong with that?" Tony shook his head, before beginning to walk upstairs again. "Try and keep the noise down. Some of us sleep here."

"I sleep." said Thomas, with an indignant pout. "Just not as much as you lot."

"If you're still down here in the morning, you know your Aunt Pepper will be annoyed." said Tony, smirking. Thomas nodded before turning back to the screen. Which was now showing images of a department store blowing up, followed by images of shop window dummies coming to life. "Damn, they didn't waste much time." said Thomas, shaking his head. Before sighing. "Sir, there is a police box on the drive." said J.A.R.V.I.S, as the screen changed to reveal a police box in between Tony and Pepper's car. A man in a leather jacket stood there, leaning against the box, with the door wide open. Showing the coral interior, with a blonde and another man stood there. Thomas let out a small frown, before standing up. "Unlock the front door, J.A.R.V.I.S. I'll be right back."


He stepped out onto the drive, as the man said "Hello."

"Finally come to check on me?" asked Thomas, looking at him. "What let you know I was still alive?"

"I came to apologize." said the man, looking at Thomas. "Son..."

"Don't you dare 'Son' me, Doctor." said Thomas, glaring at the man. "You left me to die! Before you set off the Moment, you should have found me! I VERY NEARLY DIED!"

"I don't even remember setting it off." said the Doctor, looking at Thomas. "I know I did, but... I have no memory of actually doing it."

"Doesn't mean you didn't." said Thomas, looking away from him. "How can you still call yourself the Doctor?!" The Doctor looked away, into the police box, before saying "I'll live with the guilt for as long as I'm alive. And I know it'll take a while before you trust me again..."

"Come back in a few hundred years." said Thomas, looking at him. "Then I may have forgiven you." As he said that, he saw the blonde walking towards them. "Doctor, you do realize where we are, right?"

"Oh, you've already picked up a companion." said Thomas, rolling his eyes. The Doctor just looked at him and said "And what's that supposed to mean?"

"Don't pretend you don't know." said Thomas, before turning to face the door. "See you around, father." He spat the last word, as though it was poison, before walking back inside.


"Deadlock the door, J.A.R.V.I.S." said Thomas, taking a seat back on the sofa. As Leanne walked into the front room. "Do I want to know who that was?" she asked, looking at Thomas. Thomas looked at her and said "My idiot father. Who doesn't know how to take a hint."

"You wanna talk about it?" asked Leanne, taking a seat next to him. "Mom always says it's not good to hold things inside." Thomas let out a small smile, as he looked at the screen. "J.A.R.V.I.S, do you have the equipment to scan me?"

"You will need to stand up, Sir." came J.A.R.V.I.S' response. Thomas nodded and stood up. As a green light scanned him. The scan came up on the screen, revealing his two hearts. "Oh my gosh." said Leanne, looking at it. "You have two hearts..."

"It's called a Binary Vascular System." said Thomas, looking at Leanne, as he sat down. "I'm not human. I mean I've lived on Earth for so long it's home, but I wasn't born here. Well, technically speaking I was born in a pocket universe above Mount Olympus in Ancient Greece. But I was raised on a planet called Galifrey..."


It was nearly seven in the morning when Thomas finished telling his story, using J.A.R.V.I.S for pictures and files. "The Doctor destroyed our planet and committed two counts of genocide." he said, sighing. "And for some reason, I don't care about that. Our people were getting dangerous... and the Daleks... The universe will definitely be better off without them. All I care about, is the fact he left me to die while he went to destroy the planet." He looked at Leanne. "Does that make me a bad person? Because I'm pretty sure it does..."

"How long have you two been up?" asked Tony, walking into the room. "Because Pepper's gonna have a go at the two of you." As Tony said that, Thomas looked at the clock in the corner of the screen. "Wow, that's the time? I'm sorry I kept you up, Leanne." He frowned. "Although, it's kinda depressing my life story can boil down to a nearly six hour chat..."

"How is that depressing when you're as old as you are?" asked Tony, confused. Thomas just smiled before saying "Just replay my chat with your daughter, and I'll be out of your way by the time you're finished." He stood up and walked out of the front door. Leanne quickly ran after him, leaving a confused Tony looking at the TV Screen. Which was showing a police box parked on the car park of Zuma Beach. "J.A.R.V.I.S, tell Happy to keep an eye on my daughter." he said, before walking down the stairs into his workshop. "And transfer the video to my workshop."


"Are you seriously walking to Zuma?" asked Leanne, looking at Thomas, as they reached the end of the drive. "Because Happy would be more than happy to drive us. And it'd keep Dad happy."

"I do not want to count how many times you just used happy in your sentence." said Thomas, looking at her. "And why are you still talking to me? I mean, it's not like I'm not happy, it's just... the usual response to learning who I am is people running. Even more so during the war, because they heard the stories of my dad."

"Hey, I've never met the person they all seem scared of." said Leanne, as she saw Happy pulling up to the curb. She smiled and looked at Thomas. "And anybody who can keep Stane's son at bay is somebody I want to keep around. He's scared of you."

"You really should be as well." said Thomas, as he opened the door to the car. Leanne smiled and got in saying "You haven't done anything I should be scared of." Thomas smiled before getting in as well.


They pulled into the car park at Zuma Beach to see the Doctor lay on a blanket on the beach without his leather jacket. Thomas could see the blonde in the sea, with the other man he had seen earlier. He jumped out of the car, thanking Happy, before walking onto the beach. Leanne stood at the car, as Thomas reached his father. "Hey Dad." he said, looking at the Doctor. "I'm sorry about earlier..."

"I shouldn't have dropped in like I did." said the Doctor, looking up at Thomas. Thomas nodded, before sitting on the blanket. He slipped his jacket off, and placed it behind him. "That's a nice jacket." said the Doctor, looking at the jacket. "It's what? Boxing Day?"

"Yes, the jacket was a Christmas present." said Thomas, with a small smile. "I heard London had an Auton problem, again."


Thomas spent a few hours on the beach, talking to his dad, meeting his dad's companions. Who were actually rather nice... Rose Tyler and Captain Jack Harkness. Leanne and Happy even got into the conversation.


As soon as Happy pulled back up to the Stark house, Thomas looked like he was gonna bolt. "Seriously?" asked Leanne, looking at him. "You're scared of my dad now?"

"You do realize we've been away long enough for him to have watched that entire video." said Thomas, looking at Leanne. "He won't want you hanging around me. And I won't blame him, I'm really not a good role-model for anybody."

"Let me prove you wrong." said Leanne, as she got out of the car. Thomas sighed, but followed anyway.


Leanne walked into the front room to find Pepper and Tony talking. Thomas stood in the doorway of the front door, waiting. "Where have you two been?" asked Pepper, looking at them. "I was worried!"

"We went to Zuma Beach, with Happy." said Leanne, looking at Pepper. "Thomas needed some fresh air, and I didn't want to leave him alone."

"Plus, my father was there." added Thomas, not feeling comfortable lying to Pepper. As Tony asked "You know you said you were born in a pocket universe above Mount Olympus... Does that make you a god?"

"It makes me a demigod." replied Thomas, looking at Tony. "And I completely understand if you want me to leave. I'll hitch a ride with Dad back to London." He turned to leave, as Leanne shot her dad a look. Tony looked at Pepper, who nodded, before saying "Thomas, what makes you think we'd want you to leave?" Thomas looked at him, as Tony continued "Just because you're some alien, doesn't mean we don't want you around. You seem nice, and Leanne seems to like you."

"Plus, Tony won't mind if you wanna start personalizing your room." said Pepper, looking at Thomas. "We can go and get you some clothes now, maybe pick up a few things for your room?"


As the year came to a close, Thomas sat at the desk in his room, on his laptop. He had a long thin silver tube with a red light on top of it to the left of him as he typed away at the keyboard. "Hey Tommy..." said Leanne, walking into the room. "Come on, you're gonna miss the fireworks!"

"Flashy lights and loud noises?" asked Thomas, looking at her. "No thanks. The fireworks in this era are rubbish." He realized what he said and added "No offense, I didn't mean it like that. The fireworks get better in a few years time. I hope you don't mind if I sit these out?" He looked at her, and found her looking at him with puppy dog eyes. "Seriously?" He sighed. "Fine. You win. I'll come with you." Leanne grinned, as Thomas sat up. Grabbing the silver tube.


Tony looked at the two of them as they walked outside. Pepper was already sat on a blanket, looking up at the sky. "Glad you could join us, Thomas." said Tony, smiling. "You're about to witness history in the making."

"Been there, done that." replied Thomas, with a smirk. Tony laughed before looking at his watch. "Five minutes." he said, looking at them all. "Oh man, I'm so excited."

"If these work, I'm sure you can talk somebody into making them." said Pepper, smiling. Tony looked at her and said "Oh no, if these work, they are staying firmly in our family for the foreseeable future."

"I take it you've made your own fireworks then, Mr Stark." said Thomas, as he lent on the wall of the house with a can of Pepsi. Tony smiled and said "How many times, Tommy Boy, you get to call me Tony."

"Only if you stop calling me Tommy Boy." said Thomas, looking at Tony. "You like to live dangerous, don't ya, Mr Stark. I mean creating fireworks, how many times did they explode?"

"Far too many times." said Pepper, looking at Thomas. Leanne smiled as she took a seat on the floor next to Pepper.


Thirty minutes later, they were laughing at a joke Tony told. "I have to admit, those were so much better than I remember." said Thomas, with a smile. "Although, it could be because those weren't ordinary fireworks." As he said that, his phone beeped. He took it out of his pocket, confused. "OK, I'm with everybody who has my number." He took a look at the phone, and smiled. "Oh thank the gods, I was actually confused for a moment." He stood up. "I gotta go back to my room, I've been regranted access to my U.N.I.T account. Only took a week."