Somebody on Wattpad asked for a version in which Peter either dies in surgery or nobody realizes that he has appendicitis. So, this is the version.
The first part will remain the same, but you will see when it changes.

"Tony, she hasn't come in the last 2 weeks. I'm sure she won't come within the next 2 days. We'll be fine." Pepper stared down her panicking husband. Tony ran a hand through his hair and sighed, "But, even if she does! How would you get to the hospital?" Pepper thought for a second before replying, "Peter can drive me. He just learned to drive, right?" Tony scoffed, not at Peter but at the situation. "Yeah, but Pep, he can hardly leave the bathroom for more than 30 seconds at the minute!" Pepper sighed, knowing he was right. "But, it's just nausea now, though. Right?" Tony nodded. "Right, then." Tony still looked unsure. "Tony... if Peter can't drive me, I'll get F.R.I.D.A.Y to order an ambulance. If she starts to come, I promise to ring you."

2 hours later, Tony was ready to leave for L.A for his business trip. "Oh! Let me just check on Peter." Tony rushed off to Peter's en suite. He went to open the door and he heard retching. "Pete? It's Tony." Saying no more, Tony opened the door. He saw Peter with his arms folded on top of the toilet seat, his head resting between them with a space if he needed to be sick. There was a blanket around his shoulders and a few pillows. There was also a bottle of Gatorade on the side, next to him. "Peter?" Tony let the question hang in the air, who did all this? "Pepper. She came in earlier." God, she's perfect. Tony's thought was interrupted when Peter retched again. He then groaned really loudly. Tony raised an eyebrow. "I feel like I wanna be sick... but I can't!" Tony's heart clenched when Peter lifted his head and there were tears flowing down his face. Tony handed him a piece of tissue and Peter wiped his eyes. "Pete, why don't you go to bed? I'll put a bucket in there so if you are sick, it goes in the bucket." New tears come down his face, "I don't wanna leave Pepper alone..."

"You won't be. You can sit in the room with me if you want?" Tony turned to the new voice and frowned. He was about to speak but Peter voiced his thoughts, "But Pepper, I don't wanna get you sick before you give birth." Pepper rolled her eyes, "Peter, I've had morning sickness. I know what it's like to puke." Peter actually faced her this time when he spoke, "But morning sickness is when your body cleans itself for the baby. The stomach flu will just hurt you." Pepper just stared at him. "Peter... shut up. Just come in the living room. By the time, IF, I catch this flu, the baby WILL be out." Then Pepper proceeded to pick up the blanket and pillows and waddled off to the living room. Peter glanced at Tony. "Even pregnant, she is still a force to be reckoned with. C'mon kid, I'll get the bucket, you bring the Gatorade."

30 minutes later, Tony had said his goodbyes and left, leaving a very pregnant Pepper and a very sick Peter. Pepper was sat with her feet curled up behind her, stretching her stomach. Peter was dozing next to her with his toes slightly digging into her legs. It was nice. Pepper caressed her bump and began talking when the baby kicked. Pepper's heart glowed and she couldn't help the smile that bloomed on her face. Peter rolled over in his sleep and once he had rolled over, Pepper subconsciously placed a foot on his ankle and began to rub it, like she did Tonys when he was ill.

Suddenly, Pepper felt a sharp pain in her lower back. She hissed and brought a hand to rub it. She'd been getting these pains quite frequently over the past 3 days. She'd researched it and it said it could be her body preparing for labour. "Mrs. Stark?" Pepper sighed, "It's Pepper, F.R.I.D.A.Y." There was a pause, "Ok. Pepper?" Pepper smiled, "Yeah, F.R.I.D.A.Y?" She asked, pressing a hand on her back when it began to hurt. "Pardon me for examining you without your consent, but you seem to have signs similar to that of giving birth. Would you like me to alert Mr. Stark?" Pepper let the information sink in for a second before she snapped her practical head on. Before she could respond, Peter shot into a sitting position and leaned over the trash can and threw up. Pepper rubbed his back and replied to F.R.I.D.A.Y, "No, but get a car ready. I'll go to the hospital and... actually, yeah. Say this, hey Tony, F.R.I.D.A.Y thinks I'm showing signs of the very beginning of labour. Pete is taking me to the hospital for a check-up. Don't leave until I text you what they say. Love, Pepper. That ok?" There was a pause as F.R.I.D.A.Y did her work. "Wait, What?" Peter asked once he was finished. "F.R.I.D.A.Y thinks I'm showing signs of the beginning of delivery. Tony said you can drive..." Peter rubbed his neck, looking paler than he had earlier. "I can... but I'm not sure if I can make it to the hospital without being sick," Peter admitted, sheepishly. "That's Ok. If we need to pull over, or, hell, if I need to hold a kidney dish for you to puke in if necessary, then I will," Pepper confidently spoke. "Ok then. Let's go."

Pepper kept an eye on Peter the whole time as he was known for putting on a façade when he was sick or hurt. His expression stayed the same the whole time... save halfway through and nearly there. There was no music playing and the pain in Pepper's back increased by quite a lot in the journey. Suddenly, there was a loud gulp. Pepper looked at Peter, whose expression was grey-faced and tight-lipped. Sweat was on the side of his head. "Pete?" Pepper asked, cautiously. His skin blanched even more and Pepper had a couple of seconds to shove the kidney dish under his chin before he threw up. Between the 3 heaves, bless him, he kept glancing up at the road to make sure they were ok. After the 3rd heave, he profusely apologized to Pepper for the grossness of the situation. She just replied with, "Honey, I had to deal with Tony when he had food poisoning once. And he had the shits. So that was fun!"

Nearer towards the hospital, on a quieter road, they had to pull over. This was the 2nd time Peter threw up. He stumbled out of the car and bent over, practically in half. Pepper moaned to herself as she felt another sharp pain. Peter must have heard it with his enhanced hearing because he straightened back up and stumbled back into the car. Because it was a quieter road, they could drive faster. Pepper saw that Peter looked very pale and that his arm snaked around his middle and he was slightly bent over. "Pete? Are you ok?" Pepper asked. "Yeah... my stomach just really hurts..." he trailed off, eyes squinting in obvious pain. "Peter? Where does it hurt?" Pepper asked. He gestured vaguely to his whole abdomen. Pepper bit her lip, not knowing what to say. "I think it's just my muscles that hurt. From... ya know... my throwing up." Pepper nodded, "Makes sense." The drove in silence for a few seconds before Pepper suddenly became wet. She glanced down and saw a dark spot on her trousers. "Um... Pete? I think my waters just broke."

Peter drove faster.

They got to the hospital in 5 minutes (even though from where they were when Pepper's waters went it was 15 minutes away) While Peter was parking, Pepper went to sign in. "Hello?" The nurse glanced up, looking mildly annoyed that someone disturbed her nail filling, but then she saw Pepper. "Oh, Mrs. Stark! What's the matter?" Pepper raised an eyebrow and the nurse looked down at her 9 months and 1-week pregnancy bump. "Oh... right... I'm guessing you are going to want me and the nurse that deals with you to sign an NDA?" Pepper nodded, "Just for the safety of my baby." The nurse nodded, "I'm guessing Mr. Stark is on the way?" Pepper confirmed this and reached into her bag. "Here is an NDA for you to sign now." She waited while the nurse did so, then the nurse photocopied it and gave the original to Pepper. "Oh! I just remembered, Tony had one of his personal doctors as my midwife. Alison... Micheals? Or Mitchell. One of those two."

"Alison Mitchell? Yeah, do you want me to call her down and get her to take you to your private room?" Pepper nodded and waddled over to a section of chairs and lowered herself down into one. She turned on her phone and saw 2 missed calls: One from Tony and one from Peter. She rang Tony first.

"Mrs. Stark. I was beginning to think you were ignoring me." He said in lueof greeting. "No, I'm checking in to the labour ward. Alison Mitchell is gonna come down and grab me in a bit." She replied. "How far are you?" He asked. "My water broke about 10 minutes ago."
"Is that good or bad? This isn't exactly my area..." Pepper rolled her eyes, even though she knew he couldn't see her. "It's fine, we've got at least 3 hours until I give birth, at least." Tony nodded, "Good, I'm 3 hours out. Can you cross your legs?" She swore at him and could practically hear the grin. "Love you, babe."The phone clicked off. Pepper then dialed Peter, who answered on the 2nd ring. "Mrs. Stark?" Pepper frowned. "Pete, are you ok?" The concern leaked from her voice and she couldn't help it. "Yeah... yeah...I'll be with you in a few seconds... I just need a second..." He sounded out of breath. "Peter?" Suddenly there was a wet sounding noise as if somebody was choking and a clatter. Pepper guessed he threw up and he dropped the phone. She waited. "OK... ok, I'm back. I'll be-wait, where are you?"
"In the waiting room."
"Ok, I'm coming up to it now. See you in a sec." The phone clicked off before she could say anything else. True to his word, 23 seconds later, he stumbled through the double doors. He looked horrible, he was pale and shivering. Peter calmly walked over and sat next to her. She looked at him and began to speak but he interrupted her. "Pete did-"
"Yeah. 3 times." She might ask for him to have an IV soon... he must be dehydrated. Before she could think anymore, Alison turned up and walked them to her private room.

When Peter disappeared to go to the bathroom, Pepper asked for a bucket or something that could be puked into. Alison seemed concerned, but Pepper waved it off as her just feeling nauseous, which seemed to put Alison at ease because she said that nausea was common during labour because of the pain. Alison left and said she would come back in 1 hour. When Peter, finally, came out of the bathroom, he looked significantly worse than before. Pepper was layed up in bed which left one of the two armchairs, one of which Peter flopped carelessly into. He saw the bucket near her bed and frowned, "You're not feeling sick, are you, Mrs. Stark?" Pepper rolled her eyes, "No, it's for you and for the love of god, stop calling me that. It's Pepper." Peter nodded and grabbed the bucket, dragging it closer to him. He didn't say anything for a small while but Pepper could tell that something was bothering him. "Peter, what's that matter?" She asked. "My stomach really hurts..." He whimpered, curling into a ball on the chair. Pepper made a noise of sympathy. "Tony will be here soon, so he can help you."

2 hours later, Peter was holding Pepper's hand as she battled through another contraction. Alison had come in 10 minutes ago and said she was 6 centimeters dilated. The contraction finished and Pepper was left panting on the bed. As Peter backed away to go and sit down, he suddenly felt a sharp stabbing pain in his stomach and brought his left hand up to cage it with a hiss. It drew Pepper's attention and she looked at him, "Peter?" She asked, "Fine... I'm fine." Peter ground out, the pain-reducing slightly. "Peter, sit down. You look like you are gonna pass out." Peter rubbed his head and turned to sit down when his stomach cramped and he was left heaving into the bucket. Suddenly, the doorknob twitched and clicked open. "Pepper!" Peter sighed in relief as he realized it was Tony, who made a beeline straight for Pepper, not noticing Peter. Peter tuned out their voices and crawled into the chair in a ball.

He didn't mean to, but he fell asleep.

A loud scream woke him up and he jumped into a standing position. Tony was quick to reassure him that is was another contraction. Peter nodded, swaying slightly. Pepper's contraction wore of and Tony diverted all his attention to Peter. "Pete?" He asked, reaching a handout. Peter stopped swaying and focused on Tony's voice. "Kid, what was that?" Peter was about to respond when molten agony spread from his stomach. He bent forwards, clutching it in his arms with a pained and barely contained scream. Both adults reached out for him but he fell to the ground, tears streaming down his face.

He could hear Tony shouting things and Pepper shouting things back. He was turned onto his back and there was a cold, unfamiliar hand pressing on his stomach. The hand reached his right side, and he lurched forwards, a scream left his lips and a broken sob. Something was pressed into his arm and his world went black.

5 hours later, Pepper gave birth to Morgan. They would have been ecstatic if Peter had not been rushed into emergency surgery.

Another 5 hours later, Peter's surgeon came out to see them. "Mr. Stark... I'm sorry, but we did our best. His appendix burst and began leaking into his blood. We managed to get out 80% of the infection and the organ was successfully removed... but... we couldn't complete the removal of infection for 1 reason." The doctor spoke with Tony. "That is...?" Tony asked, to which the doctor responded with: "I'm deeply sorry, but he flatlined."

"I'm so sorry for your loss."

Tony couldn't stop the tears from cascading down his face.