Peter was Pepper's son. No, they weren't related biologically, or through family marriage, but he was her son nonetheless.
Pepper grew to enjoy the company of the ever so energetic fifteen year old her fiancé had taken under his wing. Somehow, Peter managed to fill up the silence of her ever too large home with the warmth and joy only a child could bring. She was fond of his constant weekly visits, often inquiring about last nights patrol or the events of his school day.
The fifteen year old undoubtedly brought out her maternal side with his presence alone. She often finds herself sending quick reminders to eat through out the day, or making him lunch in the mornings on days he stays over, though Peter assures her she doesn't have to go out of her way for him; Obviously she doesn't listen and does it anyway. She can't count how many times she reprimanded him for breaking cerfew, or letting his grades slip to spend more time as his superhero persona.
Pepper genuinely enjoys being around Peter throughout the day, always stopping to sasay hello on the chance they bump into each other. She sometimes finds herself sitting on the couch, with Peter, on days she works from the comfort of her home. She sits on the couch with a Starkpad in hand while the boy busies himself with homework before heading down to the lab. Occasionally, she'll offer her help, especially with the business class Peter took up this year. Tony joins in too, sometimes, lending an ear on his chemistry or math.
Pepper's come to love the days she can steal Peter away from Tony, having the bubbly boy shadow her. Though she does love her job, Peter's shy yet talkative persona brings a new light to her day. She can't help but smile at how the teenager looks up at her in such admiration and delight. It's not as if no one else has before; She in fact gets the same look of adoration from many of the Stark Industries interns, but getting it from Peter makes it different somehow.
Peter always stays over on Friday nights, taking his leave that Sunday morning. Pepper often finds herself leaving office as early as she can, along with taking Saturday's off. If Tony can spend his weekends with Peter, why can't she?
Her favorite Friday's are those she leaves just early enough to catch Happy before he departs to collect Peter after school. She loves the excited look that reaches Peter's face upon seeing her in the backseat of the sleek black Audi. They conversed about Peter's day throughout the length of their hour and a half car ride. She never accounted for how much she would enjoy hearing about decathlon practices and failed them labs, but she does.
Peter and Pepper always cooked dinner on Friday nights. They used to let Tony help, but after he almost burned down the compound, he was reduced to picking out the music and passing ingredients.
They would eat like a family. Pepper would ask what they were working on in the lab and be met with Peter's energetic babbling on their latest project, an ear-to-ear smile plastered on his face. She'd have to remind him to not eat with his mouth full before he chokes. Tony would laugh and ruffle his hair in a dad-like way. Peter would whine, responding with: "Lay off the hair old man." She in response would tease the two and telling them to save the roughhousing for later. Peter would clear up all the dishes and ask about her day, his eyes shinning, while cleaning them up, dismissing their efforts to help.
In the end they'd always find themselves huddled up on the couch, watching whatever movie was picked.
Peter was squished between she and Tony, his head resting on her shoulder and legs sprawled out in her fiancés lap. She ran her long fingers through his messy chestnut curls as he yawned softly, clinging to her side. She adjusted herself, sitting to her side and allowing the boys head to fall to her chest. He sighed into the new position, a hand scooping up some of her large shirt. Pepper couldn't help but smile as Peter murmured what sounded vaguely like a I love you, mom before his eyes fluttered shut.
So, yeah. Pepper loves her baby. Biologics be screwed because she may not be his real mother, but she was undoubtedly his mom, and he would always be her son.