Title: From the Ashes

Author: Shannon – shannyfish

Disclaimer: Iron Man and Avengers do not belong to me, but Marvel Entertainment and Disney. This is for entertainment purposes only.

Rating: PG-13 (for now)

Summary: Tony and Pepper start anew in New York. Starting over isn't always so easy… Post "Iron Man 3". Tony/Pepper

Warning: none that I can think of right now!

Author's Note: I think that given what happened in "Iron Man 3" that the characters can seem to be a little rocky! I promise, if they seem bipolar, they will straighten out! :D

Constructive criticism is appreciated!

. . .

"From the ashes a fire shall be woken,

A light from the shadows shall spring;

Renewed shall be blade that was broken,

The crownless again shall be king."

― J.R.R. Tolkien, The Fellowship of the Ring

. . .

"Pepper!" Tony screamed. He'd felt like he'd screamed her name over and over again.

He hadn't expected Killian to already have so many Extremis followers. Tony had parked the armor for Pepper and Bruce to ensure that it didn't take unnecessary damage. And he'd felt so much relief when the Hulk had appeared in all his green angry splendor.

Killian had appeared with Pepper in tow. He'd seemed so distracted with Pepper that he hadn't seemed to notice their approach at first. Tony's breath felt like it had been knocked out of him when he saw Killian drop Pepper to the ground.

"Pepper!" he screamed again. He kept hoping that she'd move away so that they'd all have a clear shot. Even with War Machine and the Hulk, Tony wasn't sure if they could take Killian down. But the fact that Pepper wasn't getting to her feet worried him more.

"Tony, I've got a lock," Rhodey's voice echoed through his helmet.

"What about Pepper?" Tony asked and then a lock came up on his end as well. "I've got it, too…"

"Let's do it while Pepper is clear," Rhodey said.

But before Tony could agree, the whole where Pepper and Killian were seemed to go up. Tony didn't feel like he could move fast enough. Like he was caught in slow motion. Rhodey was at his side and the Hulk was already there. His mind flashed back to when he'd told her to let go…that he'd catch her…and then the thing she'd been on shifted just as she had let go and he'd watched in horror as she'd fallen to a fiery death. Or at least he'd thought he'd lost her.

"Be okay, Pep," he whispered as he continued to move towards where he'd last seen her.

"Scanning now, Sir," JARVIS announced. "Taking into account possibility of Extremis."

"Tell me something, JARVIS!"

"Still working, Sir."

"Work faster!" he spat. And just as he neared, he watched as the Hulk scooped up Pepper…and she wasn't moving. Hulk made a low sad sound before a loud angry roar erupted from him. Tony felt like he couldn't get there fast enough. Just as he finally got there, the Hulk shrunk down into Bruce Banner.

Tony collapsed down next to Bruce; he was still in his armor. "JAR-JARVIS!" The seconds it took for JARVIS to respond felt like a lifetime.

"Weak vital signs, Sir," JARVIS reported. Pepper's vital signs fluttered to life on his HUD.

The faceplate retracted and he remembered the other suits. He'd kept them hidden away to keep them from becoming unnecessarily damaged. He called for both of them. "She's going to be okay," he said mostly to himself as he moved closer.

"We really need to get her to a hospital," Bruce told him. "The best hospital in this area is going to be the University of Colorado Hospital in Aurora. But it's probably over two hundred miles away…"

"Not our way of traveling," Tony said and released himself from his Iron Man armor. He had his earpiece with JARVIS still in and gave him the command to open Pepper's suit up. He scooped Pepper from Bruce and just silently prayed that she would be okay. "You're going to be okay, Honey…"

"I told her I wouldn't let Killian near her," Bruce admitted. "But I had to help you… I didn't know Killian had gotten past…"

"She's okay," Rhodey said. Tony hadn't noticed when he'd gotten out of his own suit. "She's going to be okay… You did your best…"

Tony stared down at her, willing her to open her eyes as he carried her to where her suit was waiting for her. It would safely keep her, monitor her, and transport her to the hospital. Tony just hoped that it wouldn't be her final ride. He froze when he saw her lips move. He couldn't hear anything, though. "Pepper?" he whispered and leaned his ear down so that he could hear her better.

"You're late."

. . .

They'd arrived with a medical team ready for them when they landed. Tony had removed Pepper from the suit and laid her on the gurney waiting. A medical team had surrounded her and then Bruce was off and running in only pants that he was holding up. They'd gone past the area in which Rhodey and Tony could follow and it was so hard to be okay with that.

"We should call Happy," Rhodey said after they'd sat, stood, and paced in the waiting area.

"Can you do it?" Tony asked.

"Yeah…I can…"

"He's going to have questions," Tony went on a moment later. He was staring down at the floor and trying to keep from thinking negative thoughts, though they seemed to just seep into his mind just the same. "He can bring the private jet if he wants," he said.

"Okay," Rhodey responded quietly. "And Tony?"

Tony lifted his head.

"None of this was your fault. You know that right?"

"I don't know if Pepper's okay, yet," Tony told him.

Rhodey frowned at him. "Either way—"

"No," Tony said. "Either she's okay…or everything's over…"

"Tony—"

"I'm serious," Tony snapped. "The world will end… And I don't even know who would inherit Stark Industries… Pepper would know that…"

Rhodey just continued to frown. "She's going to be okay."

"How can you know that?"

"I know Pepper," Rhodey insisted. "She's stronger than any of us give her credit… And she's stubborn…she's put up with you this long… And this is the best goddamn hospital in the whole US. I even looked it up on my phone to make sure Banner wasn't out of touch. This place is the best. And Banner's back there…"

"Call Happy…" Tony said. "Please," he added a moment later as he rubbed his face.

And Rhodey was finally gone.

And it didn't help.

He couldn't stop thinking about how he'd failed Pepper. How everything was his fault. He'd had chances to give up being Iron Man. He hadn't done it. And it was starting to scare him as he thought back to when Pepper had told him she understood why he liked being in the suits so much.

After Obadiah…he could have stopped. He was too star struck, though. Too giddy with the idea of being a super hero. He'd gone on national television with the ability to deny everything and instead he'd flat out said 'I am Iron Man'. After Vanko and Hammer he could have stopped. He'd lowered his drinking considerably and he'd been given a second lease on life…but still… He knew he didn't need to be Iron Man, he was Tony Stark…everyone in the world knew who he was without the suit. And then New York… If anything, he would have thought that would have been enough… But no, he'd just felt the need to make more suits…dozens and dozens… Did they come in handy? Yes. Did that mean it was right? No. Aldrich Killian and the Mandarin (though they were really the same person) had come out of the wood works and had threatened everything in his life…including Pepper… And what had he done? Moved and had wanted to set up shop. He'd stop Pepper he could stop, but in all honesty…he didn't think he could. It was almost like an addiction…

And like any addiction, it was destroying his life…

He'd been given chances to stop and he'd made other choices…

Choices…

It seemed like that's how everything had began. He and Pepper had been discussing choices and how they'd affected their lives. Every choice they made affected what the next day would bring. And so far, he wondered if he'd made any choices differently if he'd still be lucky enough to have Pepper or would she have left him? He shuddered at the idea of a world without Pepper Potts.

"I am who I am because of the choices I made yesterday," Tony said aloud to no one.

"Eleanor Roosevelt."

Tony looked up to find Bruce standing there. He was wearing blue scrubs, which was an improvement to holding his pants up. "Yeah…"

"Why…exactly are you quoting Eleanor Roosevelt? She doesn't quite seem up your alley," Bruce said.

"Pepper…she's the one who told me that quote," he admitted. "I told her I liked 'I'll make better mistakes tomorrow'."

Bruce nodded as he crossed his arms over his chest. "That sounds more like you."

"Pepper…"

"She's okay for now," Bruce said as he sat down next to Tony. "Basically…the Extremis is fighting...cells that are healthy."

"Why do I feel like you're not telling me everything?" Tony asked.

"It's the truth," Bruce told him. "That's literally what's happening… And we've got her temperature down…her pain is down…and she's as stable as she's going to be for the moment."

"What do I need to do?"

Bruce sighed. "I put in a call to Fury. Since it's not in Pepper's best interest to move her right now, he suggested contacting Sue Storm and Reed Richards from the Fantastic Four or Moira MacTaggert who is based out of Muir Island in Scotland. He said that they would most likely be the most helpful…"

"Why can't we just deactivate Extremis?"

"It would more than likely kill Pepper…" Bruce said slowly.

"How likely?"

"Ninety percent," Bruce told him.

Tony frowned and got up. He felt the need to pace. "I need to see her," he said as he raked his fingers through his hair.

"She hasn't woken up yet," Bruce told him.

"She spoke before I put her in the suit," Tony said as he stopped and turned to look at Bruce. "But JARVIS said she'd been quiet the whole time she was in the suit…"

"What did she say, Tony?" Bruce asked as he took a step towards him.

"She told me I was late."

Bruce broke out into a grin.

"What's so funny? I don't find any of this amusing!"

Bruce waved his hand. "You don't understand… When I was taking care of Pepper… I was trying to keep her spirits up…keep her positive…she kept pushing me to leave her, but I was too afraid that she may decline without me there…and she told me that you had better hurry up because you were already late." He waited for a moment. Tony didn't think it made it any better. "She was teasing you… That's a good sign…"

Tony let out a heavy sigh. "I just… I need to see her. I need to sit with her. I need to talk to her…"

"She may not answer," Bruce said. "But I'm sure she'd be happy for you to talk to her… She can hear you even if she's asleep…"

"Were you talking to her?" Tony asked. He was curious. Bruce had been taking care of her for days now. He was thankful for it. Even though he hadn't had the contact he had wanted with Bruce, there was something comforting knowing that Pepper had been taken care of and that she had someone familiar to care for her in his absence.

"Yes," Bruce admitted. "I talked to her the whole time. I even told them to make sure they call her Ms. Potts or Pepper… Killian was trying to brainwash her or something. He would only call her Virginia…and when I first got there and I called her Pepper once he was gone…she'd flipped out so afraid that Killian would appear and kill me."

"Thank you."

"For what?"

"For being there," Tony told him. "Not just now…for Pepper…for before… For everything," he got out. "I'm glad that she had you while she was in that terrible place."

"You would have done it for me," Bruce told him. "You two have practically brought me into your little family… And that's how I think of us. Family."

Tony smiled a little. "We are family."

"Come on, let's go see Pepper," he said as he motioned towards a pair of white doors that were labeled 'authorized personnel only'. "If she hears you, she might wake up… I kept telling her that she was safe and that you were here…and you know what…I think it helped…I think it's what helped her relax…"

. . .

He didn't know if he believed that Pepper could hear him. Tony really didn't know if he was just making a fool of himself…or if it was that people just said that people asleep could hear you talking to make the person talking feel better. Because it sort of felt like therapy.

Happy was supposed to be landing…and Rhodey was off to make sure that Happy got picked up. They were also supposed to be eating and then bringing back food. So, it gave him some time. It made things easier with just Bruce there. Bruce had offered to wait at the nurses' station, but Tony had been too afraid that if Bruce walked too far away that machines would go off… And plus, he trusted Bruce. He knew what he could say in front of him.

"Hey, Pep," he whispered. He was sitting at her bedside and he was almost afraid to touch her. She was hooked up to IVs and wires. There were monitors everywhere and he figured that as long as there was steady beeping that she was okay. "Bruce says you can hear me… Not sure if that's true…but I'm going to talk anyways… Feel free to tell me to shut up anytime." He waited to see if she'd say anything.

Nothing.

She didn't even twitch. He reached out and took her hand in both of his. He just held it and tried to focus on her. "Everyone's told me this isn't my fault… But all I can think of is how this is my fault… I can find so many ways in which this is my fault... So, how can it not?" He sucked in breath and tears fell from his eyes. He hated seeing her like this. She looked so lifeless and he was just thankful that she wasn't hooked up to a ventilator.

"You've kept my life together for so long, Pepper… I don't think I've told you 'thank you' or 'I love you' or 'I appreciate you' or anything like that enough. But I do… All of it. I know I'm impossible and sometimes I can be stupid and I can act like a jerk… You of all people in this world know the flaws that I possess both past and present, " Tony continued on.

"You and I…we've made a family… Happy and Rhodey and Bruce and JARVIS and the robots… We were trying to make a new home…which I know I haven't been very helpful with… I'm far more productive when JARVIS is there… It just doesn't…I don't think I know how to explain it properly… I guess…I wanted it to be our home and I was afraid I'd make it too much into my home…"

Tony sighed. Pepper hadn't moved or said anything since he'd gotten there and he didn't feel like the talking was doing any good. He looked over to Bruce, who was still standing by the door. "This is stupid…"

"I think you should be talking to her like this all the time," Bruce told him. "It would be good for you…for both of you…"

"I don't follow," Tony said.

"You two are still learning to communicate," Bruce told him. "You're too used to doing whatever you want…and that's not how a relationship works. It's not just about the sex and sharing an apartment—"

"Mansion."

"Whatever… It's just not sex and sharing the same space… It's so much more than that," Bruce told him.

"You told me you weren't a shrink, but you're sounding awfully shrinky right now…" Tony told him.

Bruce laughed. "Maybe I just have better relationship experience than you do…or I watch Oprah…"

"Is she even on any more?"

"No idea," Bruce told him honestly. "There's Dr. Phil, though…"

"I thought he doesn't even have a Ph.D."

"I don't think he does… But he likes to give advice…and he has a TV show… Sounding like he had the education sold it."

"True."

"So, what else did you want to talk to Pepper?"

"I don't know…"

"You know…" Bruce pushed. "What have you wanted to say that you haven't said yet?"

"I…" Tony frowned. "I…" He sighed. "I wanted to tell her—"

"So tell her!" Bruce said and gestured to where Pepper was.

Tony turned back to Pepper and tried to think of the right words. He had done research on the subject and had even tried out watching videos on youtube. Apparently youtube was the place to learn new things. Tony was still used to getting information from papers and journals. He suddenly felt nervous. "I…I love you, Pepper… You know that. You are the person who is the closest to me… You've been the one person I've been this close to since I lost my parents."

He paused for a few minutes as he tried to gather his thoughts. He still felt weird about talking to Pepper like this…and yet he was nervous. "You kept me alive. You kept me from doing more stupid things than I did… You always tried your best with me. You helped me when I needed you… You kept me safe and sane. You did what I couldn't." He was quiet again. "Pepper, you've been my conscious and you're my heart… You're the real proof that I have a heart, Pepper… It wasn't ever that arc reactor… It was always you…"

"When I finally had you in my arms after we thought Killian was gone… All I wanted to do was propose… To ask you to marry me and whisk you away to Stark Tower…" Tony admitted. "But how could I? We'd lost everything we were used to… The mansion in Malibu… Our lives there… It seemed like somehow Killian had destroyed everything up until that point...because we both came out of it differently…and I know I was already messed up from New York…" He sighed and briefly glanced over at Bruce who seemed to be pretending to not be there. Tony turned back to Pepper. "When I initiated the Clean Slate Protocol…all I could think of was how incredibly lucky I was to have you in my arms again and how I'd do anything to make you happy…how I wanted a life with you…how I would give up anything and everything for you."

Tony could go on… He knew he could go on…for hours maybe. It didn't make this any easier… And he didn't know why he was so nervous… Pepper was asleep… Why did it matter to him? He held onto her hand with both of his and leaned down and kissed her hand for a moment. He rested his forehead against it. Tony closed his eyes and prayed to whatever Gods were above that Pepper would wake up. They could take him if that meant that she were to live. All that mattered was Pepper…

Tears ran down from his face and onto her hand. "Marry me, Pepper," he whispered.

He stayed like that for a long time. He just kept wishing for her to wake up. For her to whisper a response.

Anything.

Anything at all.

He would be happy to hear her tell him to go away or to shut up.

Anything was better than nothing.

And his mind couldn't help, but go to the worst-case scenario.

This was his fault.

He wouldn't blame her if she never forgave him.

He'd put her in danger.

She deserved so much better than him.

She should be happy.

More tears fell and soaked her hand. He didn't know what else he could do. He had said everything that he could think of saying. Even things that he'd not intended on saying… It hadn't made any differences. The monitors all beeped the same. Pepper hadn't moved. Pepper hadn't opened her eyes. Pepper hadn't said anything. The people who said that people in comas (or asleep) could hear you…they were wrong. It was just a lot of talk. It was something to make the person talking feel better… It was therapy, but without the shrink.

God, he loved Pepper.

He didn't want to lose her.

He didn't think he could stand losing her.

He knew what it felt like, even if it had been for minutes, to lose her…and he didn't want to feel that empty and so dark…

Never in his life had he felt so passionate about another human being.

Pepper Potts. The woman who had found a mistake in his numbers. The woman who he knew the moment he'd met her that she was meant for better things… The woman who had taken care of him and kept him alive… The woman who had cleaned up all his mistakes… The woman who ran his company… The woman who saved his life…and held his heart… She was the most rare treasure…in his life and in the world.

"Yes," was barely audible.

Tony stopped and looked up. He looked over to Bruce, who hadn't seemed to hear anything. Was he going crazy? Was he hearing things? He wouldn't be surprised if he was losing it…or having a breakdown. Another breakdown.

"Pepper?" he whispered as he squeezed her hand lightly.

"Yes," she whispered.

Her eyes were still closed, but he noticed Bruce move that time. He wasn't hallucinating. She was talking to him. "I'm here, Honey," Tony told her. He kissed her hand again as he continued to hold it. She squeezed every so lightly back in response and a smile spread across his face.

It felt like for the first time…in he didn't know how long now…he'd felt like things were going to be okay. He could only assume that this was a good sign. He'd have anyone who could possibly fix what Extremis was doing brought there… He didn't care if he needed to fund a whole new hospital building, he'd do what he needed to do to ensure that Pepper received the best care.

"I'm here," he whispered again.

His lips were on her hand again and then moved up to press a kiss to her forehead, his hands still holding onto hers. "I'm here…"

Her eyes fluttered open, but only halfway and stared up at him. She looked almost surprised, but definitely not disappointed. She reached up and Tony noticed how much effort it took her to do so, Pepper placed a hand on his cheek. "You're okay," she whispered weakly. A small smile formed on her face.

"I'm fine," Tony said, his voice cracking. She was so worried about him. It didn't seem fair. She was always concerned about him…it was never about her. And he knew he needed to make more things (besides saving her when bad guys were around) about her. Tony knew that he needed to show Pepper exactly how much she meant to him…for her to be in his life.

"Good," she whispered, her smile still shining.

"You're better…but you're still sick," Tony whispered. "Do you remember?"

Pepper nodded ever so slightly and then her smile brightened a bit. "Hi Bruce," she whispered.

"Hi," Bruce said.

Tony looked over his shoulder. Bruce was standing right there looking a bit nervous. As much as Tony wanted this time with Pepper, he was thankful that Bruce was there. It made him worry a little less. "Happy and Rhodey are on their way," Tony said. "We've all been waiting for you to wake up…"

"You shouldn't fuss," Pepper told him.

Tony leaned in and kissed her. After a moment, he leaned his forehead against hers and allowed the tears to fall from his eyes. "Let us fuss…"

"I'm just happy you're okay," Pepper said. Her other hand, which he'd been holding moved up to grab the front of his shirt. She held onto it for as long as he kept his forehead against hers.

"Extremis isn't behaving right now," Tony said. "And Bruce said we still can't turn it off."

"I know," Pepper whispered.

"You don't know everything," Bruce spoke up.

Tony turned to Bruce. He knew that there was something else. Something that Bruce wasn't telling him. Tony didn't know why he didn't tell him before. Maybe Bruce felt like he could only tell them both, he didn't know. Maybe Bruce didn't want to scare him anymore before he'd seen and talked to Pepper. Tony just hoped that it wasn't more bad news. He didn't think he could handle anymore.

"You might want to sit back down," Bruce told Tony.

He didn't like the sound of that. Tony sat back in his chair and held onto Pepper's hand. "What is it?" Tony asked. He tried to prepare for him to say something that was going to make him break down. He couldn't do that. He needed to be strong for Pepper.

"I didn't lie to you," Bruce started off by telling Tony. "Extremis is attacking healthy cells…"

"But?"

"But the healthy cells…" Bruce said and then dwindled off. "Pepper, you're pregnant… They think around eight weeks or so…"

Tony was sure his eyes had widened and he was thankful that he was still staring at Bruce. He didn't want to give Pepper the wrong idea. He pulled in a breath and swallowed. That wasn't the news he'd expected. He turned to Pepper who just looked overwhelmed. "Hey…" he whispered and reached out with his free hand to cup her face. "Breathe…"

"I've had coffee…and I've hardly eaten…and—" Pepper started to babble.

"The baby looks okay right now. Your body has been effectively fighting Extremis for now," Bruce told her.

"For now?" Pepper asked. "But it could kill the baby?"

"Yes."

And his gut started to turn. Tony laid his forehead against her hand. He didn't want to have to leave her. He wanted to stay there and reassure her that everything was going to be okay. He wanted to discuss this child…this child that they hadn't planned for. Was he worried? Yes. Was he happy? Beyond so.

Tony looked back up at Pepper, who just looked worried. "I'm going to need to make some calls," he whispered. "I need to get people on planes…"

"I know we've discussed who can be called out to help," Bruce said. "I just wanted to put out a suggestion now…"

"Why do I think I'm not going to like it?" Tony asked as he just stared at Pepper.

"Instead of disabling Extremis or trying to get rid of it… I think we need to accept facts. It was stable in Pepper's system… If it didn't see the baby as something foreign, then it wouldn't be fighting Pepper's system so hard," Bruce told him. "We need to consider pretty much re-writing Extremis into not fighting what is actually something natural…"

"You talk about it like it's a computer program with a line of code that has to be tweaked…" Tony told him.

"And to Sue Storm, Reed Richards, and Moira MacTaggart…that's what it's going to be…except we're talking about a virus and altered DNA…"

Pepper reached out and stroked Tony's cheek. "Make your calls… Take care of what you need to… Bruce will sit with me until you get back."

"Why does it sound like you're ordering me around?" Tony asked lightly with a small smile.

"Someone needs to make sure you're doing what you need to," Pepper told him.

Tony looked back over at Bruce. "You heard the boss."

Bruce nodded. "Not going to leave me sight."

And with great hesitation and so much strength, Tony forced himself out of the chair, allowing Bruce to have it instead. He was Tony Stark and he was about to move mountains to ensure that Pepper and their child were both okay. And he'd do it, no matter what it cost.

They were going to be okay.

. . .

TBC…