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I Have Seen Irrevocable Damage Done

Summary:

“Tony…please—” Steve raised his hands in a gesture of surrender.
“You better beg for forgiveness, Cap. Maybe then I’ll consider not sending you back to Ross in a BODY BAG!”

TLDR; Peter gets hurt after getting mixed up with the rogue Avengers, and Tony blames Steve.

Whumptober 2025
Day 01: "Please Don't Cry" | Beg for Forgiveness

Notes:

(See the end of the work for notes.)

Work Text:

Pepper had warned him not to get close to his interns. Keep things professional. Be involved, but not too involved. Every time Tony Stark had gotten too close to a Stark Industries employee in the past, it ended badly. Obadiah Stane. Quentin Beck. The list went on and on. But in all fairness to him, Pepper gave him permission to be slightly more involved with the new division of high school interns she suggested the company hire. She thought it would be a great way to do outreach and support the country's bright young minds.

After a long interview and application process, ten interns were hired from around the country. One of those interns managed to worm his way into Tony’s heart despite his efforts not to be too involved: Peter Parker, a 14-year-old kid from Midtown Tech. About two weeks into the internship, he noticed the kid staying later than the others, lingering despite being done with his tasks. Naturally, Tony approached him, being the curious person he was.

“You know you’re free to go, right?” Tony teased, leaning against the lab table where Peter stood hunched over, writing out a few formulas.

“Hm?” Peter asked, the joke not really registering.

“I mean, I imagine you have homework, folks at home that might think I’m holding you hostage. I mean, don’t get me wrong, I appreciate the overzealousness, but according to Pep, I can’t give interns overtime so—”

“You don’t have to pay me extra. I just…I need this right now,” Peter continued to work out equations on his scratch paper, erasing and rewriting.

“Ah, so you’re like me. A workaholic in the making. It’s a chronic condition, I’m afraid. Incurable. Or maybe those with it just prefer not to be helped. I mean, I’d never willingly admit to treatment, but I guess the responsible thing to do would be to hypocritically discourage it.”

“I…don’t really want to be home right now.” Peter faltered, momentarily setting his pen down, but keeping his eyes set on his work. “My uncle died last week, and my aunt’s been working overtime to avoid the empty apartment. I guess I kind of am too…” He admitted, voice quieter than before.

Tony wasn’t expecting that kind of response. For once, the man is speechless, unprepared for the level of vulnerability and severity. After taking a moment to collect his thoughts, he replied.

“Stay as late as you want, kid. I’ll be here all night anyway.”

From that moment onward, Peter Parker often stayed later than the other interns. After a few weeks in, he’d even been asked to work with Tony in his personal lab at Stark Industries.
A few months in, Tony asked him if he’d be interested in working at Avengers Tower. Night after night, they found themselves working together, getting to know each other, and thus, Tony found himself getting too involved.

Little did he know that inviting Peter to the tower would be the biggest mistake he’d ever make.

* * *

Tony had been out of the lab for once in his life, getting ready for a press conference in his room at Avengers Tower, when an unexpected guest stumbled into his doorway.

“Stark.”

The familiar voice sent chills down his spine, the kind that left you with a full-body ache, a sickly feeling.

“Rogers,” Tony replied coldly, keeping his eyes fixed on his own reflection in the mirror, adjusting his shirt collar. “Correct me if I’m wrong, but I’m pretty sure you’re a war criminal now.”

“We need your help.” Steve took a step inside the room, dressed from head to toe in his discolored Captain America suit, a beard starting to grow on his face.

“I thought Friday had removed you from her database by now. Guess I’ll have a talk with her after this, make sure she bans you from entering the premises from this point forward.” Tony adjusted his cuff links, not giving Steve any acknowledgment.

“You know I wouldn't be here if it wasn’t important.”

“Alright, Steve. What is it that is so important?” Tony said in a sarcastic tone laced with venom. He finally turned toward the man, staring him down with a dark and unentertained gaze.

“We need someone to help us hack into the security of a potential HYDRA research base.”

“Potential base? All of those are long gone. Fury made sure of it. I mean, wasn’t that the point of all those missions back in 2015? You know, the Maximoff twins?” Tony walked over to Steve, chuckling lightly in arrogant disbelief. “Only ever coming to me when you need something. Why am I not surprised? Show yourself out, Rogers.”

“You won’t even hear me out?”

“I’ve heard enough.” Tony headed back to the mirror, fixing his hair. “Goodbye.”

Humbled and dejected, Steve made his way down the stairs and back to the main level of the penthouse, frustrated with himself for even attempting to seek the help of an old friend.

As he headed toward the elevator, he passed the main lab. Steve paused after passing the room, almost certain he saw someone in there. He backpedaled slowly and glanced inside.

A young man stood at one of the lab tables, tinkering with a piece of tech and inputting something into a nearby tablet. He paused his work and looked up, feeling another presence in the room with him.

“Captain America?” Peter stammered in disbelief at the sight in front of him.

Steve hesitated for a moment, then decided to enter the lab and approach the kid against his better judgment.

“Who are you?”

“Oh, uh, I’m a Stark Industries intern. Mr. Stark has me help out here sometimes, too.”

Steve’s eyes wandered across the technology and blueprints set out on the table before him. Everything looked extremely high-tech, like another language. Whoever this kid was, he had to be smart. Tony Stark wouldn’t hire someone on the younger side unless they were a genius.

“You’re good with tech? Well, I mean, obviously, you are if you’re here…are you familiar with hacking? By-passing systems?”

“I mean, I’m familiar with it. I’ve built computers in the past. I know coding, and I’ve ethically hacked before.” Peter’s eyes hesitantly met Steve’s. “Why…?”

“The Avengers need help bypassing a HYDRA security system. If you agree to come with us, we’ll protect you. Make sure you stay out of the action.”

“You want me to be the guy in the chair for the Avengers?” Peter asked in shock.

“I do. We could really use a ‘guy in the chair.’” Steve returned his shocked expression with a small smile.

“Wait…does Mr. Stark know about this? Does he even know you’re here?”

In that moment, Steve could have been honest. In hindsight, he realized he should have. Instead, he decided to tell half the truth.

“Yes. He knows I’m here. I just spoke with him. I’d ask him, but he’s busy with a conference, so I figured…”

Peter’s eyes lit up, and Steve discussed the rest of the plan with him as they exited the building.

* * *

Tony was about to go on stage for the press conference when he received a call from a contact he thought he’d blocked: Steve Rogers. His first instinct was to ignore it, but for some reason, something stopped him from acting like himself. He impatiently answered and lifted the phone to his ear.

“I’m about to go on stage, so this better be something worth—”

“Tony, I’m sorry. I’m so sorry.” Steve cut him off, panicked and voice wavering. It unsettled Tony enough to have him pause and listen. “I brought the kid on the mission in your place.”

“What?” Tony felt his heart drop to the floor.

“On my way out, I saw him working in the lab—I said he could come with us, keep his distance. He was excited, and it seemed harmless—I didn’t think—”

“What. Happened.” Tony was already waving off his attendants and speedwalking toward his suit.

“There were more guards than we anticipated. They had biological weapons…”

Tony suited up, transferring the call to his helmet. He simmered with anger, but his concern and need for details kept him conversational.

“I’m tracing the call. Now tell me. What happened?” Iron Man jetted off into the air.

“I don’t know…I really don’t know. They injected him with something. He’s barely responsive.”

“How did you even let them get close enough to—How could you go behind my back and take an intern—He’s not a HYDRA assassin!” Tony’s voice went up the octave as he roared at Steve over the phone.

There was a moment of silence on the other line before Steve spoke again.

“We’re doing everything we can, Tony. I’m really sorry.”

* * *

Tony felt his knees give out as he landed beside the Quinjet, his suit the only thing keeping him grounded. He hurried up the ramp and into the jet to find the rogue Avengers gathered around a cot. Everything was quiet in Tony’s head, the background noise mumbled, his heartbeat thrumming loudly above it all. He swayed a little as he took in the sight of the pale and unconscious teen lying there before him.

“Friday. Vitals.”

Friday scanned the kid and sent him the results.

“Peter Parker was injected with a bioengineered substance. It has spread throughout his body and is binding to his DNA. It looks to be an experimental substance, and his body will either reject it or allow it to bind. The chemical reaction has sent his body into a coma. There is a 17% chance he will wake up due to the nature of the chemical in his system.”

Iron Man stood in silence for an excruciatingly long minute. Then, without warning, he lunged at Captain America, violently slamming him into the side of the Quinjet and pinning him to the wall.

“I’M GOING TO KILL YOU!” Iron Man raised his repulser to Steve’s face. He barely managed to pull out of his grasp and out of the way as the beam hit the wall, where the man’s face had been seconds before.

“Tony…please—” Steve raised his hands in a gesture of surrender.

“You better beg for forgiveness, Cap. Maybe then I’ll consider not sending you back to Ross in a BODY BAG!” He rapid-fire blasted at Steve, hitting him several times, missing him several times. The other Avengers ducked out of the way as Iron Man chased Steve around the jet. He tackled him to the ground and held him by the wrists tightly with his gauntlets, squeezing hard enough to fracture.

The movement of the jet and Captain America struggling against him was enough to wake up Peter momentarily. His eyes flickered open, dazedly searching the ceiling, squinting at the unfamiliar light.

“Hello…?”

The sound of his voice caused Iron Man to drop everything. He got up back on his feet and hurried to the cot, lifting his face mask to look at Peter.

“Hey, kiddo. I’m here to get you out of here.” His voice was much softer than it was moments before, yelling at Captain America.

“What happened…?” His eyes threatened to close again, and he winced, feeling the effects of the chemical in his body.

“You were injected with a bioengineered substance, a new weapon HYDRA was working on. You’re probably feeling sleepy because your body’s fighting with it.” He paused. “Either your DNA will accept it…or reject it…”

“If it rejects it…?”

“Just hang tight for me, kid. I’m going to take you back to Medbay, call your aunt. I’ll fix this.” He lifted his face mask down again and scooped Peter up into his arms, shooting off into the sky, not waiting for a response from the Avengers.

* * *
An hour later, a worried aunt paced around the Medbay waiting room. The moment Tony entered, she lashed out at him.

“How could you let him get mixed up in all of this?? He is not an Avenger! He’s not one of your superheroes you can send off to their deaths—he’s a teenage boy. He’s my boy!!” May pushed Tony with a finger to the sternum as she bellowed in his face, understandably hysterical.

Tony let her take her anger out on him, feeling it was deserved. He’d forever blame Rogers, but he’d never miss an opportunity to doubly blame himself. He should have known Peter would be in the Tower at the time he’d spoken with Steve. He should have monitored him more carefully, made sure their paths didn’t cross.

“If he ever wakes up from this—I can’t believe I’m saying this—this coma, I never want him to be involved with you or the Avengers ever again!” And with that, she hurried back to Peter’s Medbay room, tears threatening to fall from her tired traumatized eyes.

* * *

After two weeks of Medbay care and no sign of improvement or deterioration, Peter was sent home, still in a coma. Tony sent with him all the technology and medical equipment May would need to care for him.

After two more weeks of no sign of life from Peter Parker, Tony started to look for the rogue Avengers. They had gotten better at hiding, but he was determined.

After two months of searching, Tony received a call from May Parker late at night.

“Hello?” Tony asked from where he sat in his lab, working on his latest suit. A silvery-almost white suit with a cyan arc reactor.

“Tony—he’s gone. He’s gone—they must have taken him!”

Tony sat up, pausing his tinkering.

“Who took him?”

“Earlier, I swear I thought I saw Captain America outside, in the alley across the street.” May walked over to her window, peering out of the blinds but seeing no sign of anyone in the alley. “I brushed it off. It’s late. It could’ve been anyone…But I just went to check on Peter, and his bed is empty!”

Tony hurriedly typed some commands into his holographic tablet, having Friday pull up all of the street cameras in Queens. He knew how good the rogues were at avoiding cameras, but they weren’t that good. He knew they had to be captured on tape somewhere, and they were. Not too far from Peter’s apartment in Forest Hills, Cap was spotted slipping into a parking garage in Astoria.

“I found him.” Tony set down his tools. “I’ll call you back, May.” He hung up and sat back, expanding the holographic screen with his hand, replaying the footage, and zooming in on the heroes caught on film. He could recognize Captain America, but there was a second with him, someone he’d never seen before, dressed in what was a sorry excuse for a suit. It looked more like red and blue pajamas. Maybe a new ally of Rogers…

Tony swiped the screen away and suited up in his new suit. He’d been working on the superior model, saving it for the day Steve Rogers stepped foot in New York again.

“Friday. Set the route for the most recent location of Captain America and his rogue Avenger.”

* * *

Iron Man soared through the sky, a silver bullet above the New York skyline. Fury bubbled inside of him as he made his way closer and closer to the location Friday had set into his GPS. When he got his hands on Rogers…

Iron Man stopped mid-air, hovering above the parking garage.

He’d have to settle for the next best thing.

There, in unmissable red and blue, tucked behind a car at the top level, was the new member of the circus.

He dove down, like a bird of prey, and zeroed in on the new hero. He grabbed him and swooped upwards, keeping him in his grasp and barreling toward the sky at record speed. The masked vigilante thrashed in his grasp, instilled with panic, trying to break away until he looked down, realizing it was better to hold tight.

“Where. Is. He.” Iron Man’s menacing metallic voice asked.

“Who?” Spider-Man replied, breathlessly, barely a squeak.

Iron Man dropped him without warning.

Then, like a deranged cat toying with its prey, he swooped back down and grabbed him once more, flying and at record speed across the skyline.

“Holy—stop! Stop! Please, stop!” Spider-Man pleaded, gripping on tightly to the silver suit.

Iron Man switched directions, blasting toward the sky once more.

“Where. Is. He.” He repeatedly, more impatiently than before.

“Who?!” The masked teen all but cried. “Steve Rogers??”

Iron Man dropped him again, this time letting him get closer to the ground. Then, at the last second, he scooped him up and tossed him onto the roof of a nearby building. The masked vigilante rolled and came to a skidding stop at some piping on the roof. He pulled himself up to his elbows and knees, only for an iron boot to push him back down again.

“Why are you doing this?” Spider-Man asked sadly.

“I really don’t like repeating myself.” Iron Man raised his gauntlet, firing his repulser at Spider-Man’s shoulder. He pressed down harder on his back, causing the vigilante to cry out.

“You’re hurting me—”

“Where is Peter Parker?”

“Peter…” he scoffed tiredly, in disbelief. “It’s me!”

Iron Man hesitated, watching him closely. He lifted his boot from his back and took a few steps back.

Spider-Man put his hands up in surrender as he slowly sat up. He reached for his mask slowly, and Iron Man lowered his gauntlet at the sight of the teen before him. His eyes were glossy with tears.

“Please…please don’t cry. I didn’t know it was you…I wasn’t trying to hurt you.” He sniffs and takes a pause, reaching for a snarky remark at the wrong time as always. “What the hell are you wearing?”

“I could ask you the same thing.”

Tony let out a deep sigh and deactivated his suit, the nanotech disappearing into his watch.

“You could have killed me,” Peter said with grave seriousness, realizing the gravity of the situation as the words left his mouth.

Tony looked off to the side, rubbing his left elbow.

“I know…” he turned back to meet Peter’s eyes. “I’m sorry. If I’d known it was you—”

“—So Cap was right? You were hunting him down to kill him?” Peter stood up.

“Yes. And why do you have a problem with that? He nearly killed you. Actually, why are you running around town with him in a set of pajamas?” Tony approached Peter slowly as he spoke.

“Because he was trying to help me.” Peter sighed, exasperated. “I woke up a week ago. You know that bioengineered serum they stuck me with? Turns out it gave me powers. I didn’t want to tell May, hell, she doesn’t even know I woke up. I didn’t want to tell her what happened until I had it figured out. I tried to sneak out to tell you, but on my way out of my window one night, I saw Captain America in the alley across the street. Apparently, he’d been monitoring my apartment, worried and feeling guilty. Since he also had experience with HYDRA serums, he said he’d help me figure out my powers. So I’ve been hiding it, lying in bed, and sneaking out to figure these powers out.”

“You could have come to me.”

“I know…I was going to…tonight, actually. Until Cap realized you were on our trail. I wanted him to come with me because I wanted you two to finally work out your differences.”

Tony scoffed.

“You don’t have to be my interventionist, kid. You’re my intern, not my therapist.”

“But I felt responsible. Because of me, you want to kill Captain America.”

“What happened wasn’t your fault.”

“He asked if I wanted to go, and I said yes.”

“Because you didn’t know I was against it. You didn’t know the gravity of the situation—”

“—But what if I did? What if I had gone anyways? Just…let me do this. Talk to Cap. Before one of you does something irrevocable.”

Tony paused, thinking it over. Normally, he’d brush off the elevator pitch of reconciliation if it had been given by anyone else. But he couldn’t shake the guilt burning inside of him, the guilt that he felt from the kid’s gaze. He knew he was right. He’d nearly killed him by mistake, and now all he asked in return was for him to make things right with someone he once called a friend.

“Alright. I’ll talk to Steve.” He lent Peter a hand, and the teen accepted, getting pulled to his feet. “But one more question. Why the getup?”

“I threw it together the other night. Cap said I’d need a super suit once I figured out my powers.” Peter shrugged. “I went for a spider theme since I have spider powers.”

“Yeah, when this is all over…you’re getting something a little more sustainable.”

And with that, Tony let Peter lead him off to face reconciliation and forgiveness head-on.

Notes:

If you read my completed Whumptober series last year, you’ll know that I typically end each fic with two author’s notes, one that I read at the time of writing it, and one at the time of publishing. Well, Past Me talking, it is currently August 28th, and I thought up this idea late last night, in a feverish haze while listening to the Whumptober playlist. Would this have worked better as a long multi-chapter fic? Maybe. BUT it’s Whumptober and I have 31 prompts to get through, so I’m trying to keep these short. If you haven’t guessed already, this year’s duo I’ll be focusing on is Peter and Tony. I have a lot of ideas already planned out, some featuring other characters like this one did (Steve), and others simply about the two of them. I hope you stay tuned. I promise, they only get Peter. There are a few ideas on my list that I have wanted to write for MONTHS, but have been waiting to attempt them. Now I have the excuse to let my imagination run wild. This one was very much a spontaneous AU. Get ready for some even whumpier and well-thought-out ideas this October!

Also, for anyone curious, the title is a quote from the Greek tragedy, Medea. I’ve been reading a lot of Greek mythology lately. Also, whilst writing this author’s note, a rave has started across the street from me. RIP my sleep schedule.

10/1/25 - Soooo I ended up writing a handful of prompts, but I’m not sure if I’ll make it to completionist by the end of October because…I got a new job!! A really great job :) I’ve been busy with that for most of September and now October as well. However, if you guys like the prompts I have pre-planned, I will continue with Whumptober, even after October! Let’s start the Irondad revival!

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