This is set after Tony returns in the first Iron Man (2008)
As soon as the glass doors to Tony's large and extravagant home closed behind them she took off, heels clicking loudly on the floor, leaving a very bewildered and confused Tony Stark standing alone by the doors. She stumbled up the stairs and into one of the many guest rooms, chest heaving as she struggled against the emotions building up inside of her, clawing at her resolve in attempts to escape.
"Pepper!?" His worried scream of her name reached her ears and she flinched, slamming the door shut and locking it before staggering away from it and collapsing on the bed. The woman reached out and grabbed a pillow, dragging it over to her chest and hugging it securely as the tears freed themselves and slipped down her cheeks.
She choked when she tried to breathe, and pressed her face into the pillow, not caring that her makeup would smudge the white fabric; Tony was rich, he could just buy another one. The woman kicked off her high heels and brought her legs up onto the bed, eyes slammed shut, ignoring the sound of the seams of her skirt tearing apart.
Tony scrambled up the stairs as fast as he could and immediately rushed to the room she was in, grabbing the handle and twisting. When it didn't open he raised his hand and knocked on the door
"Pepper!" he cried through the door "Let me in!"
The woman ignored him, though, so the brunette resorted to Jarvis for help.
"Jarvis can you please open the door?" he requested
"Jarvis don't!" Pepper protested immediately
"I am sorry, Miss Potts, however my programming is to listen to Mr. Stark" he responded
There was silence, then a click, and the door popped open. Tony reached out with his good hand and carefully pushed it open, his eyes widening at the sight of his personal assistant curled up on the bed. He pushed the door closed behind him and locked it.
"Jarvis" his voice was low
"Sir?"
"Lock the house. If anybody comes, I'm not home"
"Very well sir"
Tony said nothing in response, making his way towards the bed. He -ignoring the doctors orders- ripped off the sling cradling his arm and tossed it away, crawling onto the bed, flinching slightly when he put too much weight on his injured arm. He stopped beside Pepper, frowning as he reached out and gently placed a hand on her shoulder. The woman raised her head, gaze meeting his. His eyes widened at her puffy eyes and the obvious tears streaming down her cheeks.
"Pepper?"
The woman turned her head away, and he reached out, gently cupping her cheek to turn her head back in his direction. His thumb gently slipped across her cheek, wiping away the tears.
"Mr. Stark" she responded
"Pepper, what's wrong?"
The woman's watery gaze flicked away from his own, and his eyes widened in understanding when she shook her head. She was scared.
Pepper Potts was scared because of him.
"I-" she broke off, unable to continue her sentence
The brunette took off his suit jacket, wrapping it around her shoulders before he pulled her carefully into an upright position and into his arms. The woman's hands came up and rested on his chest, unsure whether or not she intended to push away or pull him closer. The decision was made for her when her small hands dug into the fabric of his shirt, clutching it with all of her strength as if he might disappear if she let go.
"I was so worried!" she cried out as he head fell forward to rest on his chest "I thought you were dead!"
Tony's grip on the strawberry blonde tightened substantially and he leaned down slightly, resting his cheek atop her head.
"Pepper, I'm okay" he whispered
"No you aren't!" she protested "You have that- that thing in your chest!" she jerked away to stare at it
"That 'thing' is keeping me alive, Pep" he said softly
"Tony-" she attempted to protest
"Pepper I'm okay" he offered her a reassuring smile "I promise. I'm not going anywhere" he took her hand and pressed it against his chest, above the arc-reactor "Feel that?"
The woman was quiet, gaze fixed on the glowing blue circle in her boss' chest. The device seemed to hum under her touch, but beneath that she could feel his heart beat, firm and steady in his chest.
"... Yes" she answered slowly
"I know it's different" he nodded "And weird. But It's keeping me alive"
"I... I know" she whispered, leaning back in, her hand remaining in place as she rested her head on his shoulder instead "I just... worry" she admitted softly
"It's in the job description, if I recall, Miss Potts" he offered in an attempt to lighten the mood
A small laugh managed to escape her
"Is it now? You must have added that after I signed it"
"Is that so?" he smirked down at her
"It is" she was quiet for a moment "I..." her free hand wrapped around his waist, and her hand covering the arc-reactor slipped up to wrap around his neck gently "I'm glad you're okay, and home safe, Tony"
"Because you hate job hunting, am I right Miss Potts?"
"Yes, that's it" she pulled away and pressed a gentle kiss to his cheek before standing. She made her way to the door and opened it before turning to face him "Shall I call Obadiah for you?"
Tony was quiet for a moment
"Miss Potts, I think I would rather have some tea" he stood and made his way to the door, slipping out the opening and heading towards the stairs "Care to join me?"
"As you wish, Mr. Stark" she smiled knowingly and followed him down the stairs