This is after infinity wars, and Peter is/was Tony's biological son.
As per request, by @AnotherOneBiteADust
Hope you like it!
In the months after the decimation, and the tyranny of Thanos, people tried to pick up the pieces.
The avengers, and all available resources worked on finding the mad titan, but citizens were rebuilding their lives.
In the words of Steve Rogers, they tried to move on.
Major businesses kept running.
Schools still functioned.
Including Midtown Tech.
Who were, in fact, taking a field trip to Stark Tower.
Tony Stark hadn't been seen in public since the day Thanos' minions came to earth.
He had returned, but had not left the tower.
The students were hoping to catch a glimpse of the reclusive billionaire.
Ned and MJ didn't look forward to going.
MJ was sick of Flash trying to prove that Peter was a liar.
She missed Peter. He hadn't come to school in months, and Flash was making it even worse.
Taunting them about how their loser of a friend was too afraid to show up, to be proven wrong.
Which made MJ's blood boil.
She was the only one who could call them losers.
Because they were her losers.
Protective much?
You could say so.
Because Ned and Peter were her only friends.
And heck to the no was she letting Flash tarnish Peter's reputation any more than he already had.
-----------
Surprisingly Flash left them alone on the bus ride to the tower.
It may have something to do with MJ whispering something in his ear that made him turn pale and gulp, but whatever.
The building wasn't as busy as it should have been.
A tour guide met them at the entrance, her smile practiced but tired. "Hello. Midtown I assume?"
The teacher, Mr Harrison, nodded. "Yes."
She waved her hand toward the scanner. "We have your guest badges over here."
They followed, most of the class gaping at their surroundings.
The woman pinned her own badge to her shirt, the laminated paper showing the name Lindsey.
She led them through the ground level labs, then to the higher ones.
Flash was suspiciously quiet, occasionally throwing the odd glance at Ned and MJ.
They were on one of the main level labs, looking at some non-classified schematics when Flash finally spoke up.
"Do you know Peter Parker?"
The question was aimed at Lindsey, who looked surprised. "I'm sorry, I don't know anyone by that name. I'm new here, you see."
Flash didn't say anything else, but MJ could tell by the glint in his eyes that he was far from finished.
------------
It all came to a head when they spotted Tony Stark.
The class immediately started clamoring, getting his attention quickly.
He waved his hand at the person he'd been talking to, and walked slowly to where MJ and Ned were standing. "Hey Scary girl. Fred."
MJ gave him a small smile. "Hey Tony."
Ned echoed her welcome.
MJ could tell that Tony was in a daze, eyes unfocused.
She tapped his shoulder. "Tony? Are you okay?"
He stiffened, then sighed, all the tension leaking out of him. "Yeah. Sorry. Just tired."
MJ shifted her feet. "Do you- was Peter-? Is he here?"
He understood what she was asking, and his expression shuttered. "He's gone."
Flash had to speak up then. "So, Mr Stark," he began, sounding pompous. "I'm sorry to inform you about this, but someone has been tarnishing your reputation. A class mate of ours was spreading lies about having an internship here. His name was Peter. Peter Parker. I'm sure you would like to get this taken care of as quickly as possible. The liar hasn't shown up in weeks, and I'm assuming it is because he knows he has been found out, and his lies exposed."
He clearly expected a reward, his self-justified expression speaking for itself.
What he didn't expect was a punch to the face that sent him slamming into the wall, and then to the ground.
Everyone gaped at the scene.
And at MJ, who was shaking her bruised hand. "Wow. That felt really good."
Tony Stark stepped forward, going to his knee beside Flash.
His hand gripped the collar of Flash's shirt, twisting it in his fist until they were eye to eyes.
Flash gulped at the pure, unrestrained fury that was directed at him.
Tony's voice was low, and dangerous. "He is my son, so you shut it. Got it? Shut. Up. I don't give a crap about if you're a minor, I will. kill. you. Do you understand me?"
Flash gave a terrified nod.
Tony leaned in, eyes glittering with hatred. "Now you listen well, Eugene. I never want to see you in my sight again. I never want to hear another word from you, and I never want to see you in this building. When I get Peter back, you are not to touch him, speak to him, or even look at him. Do I make myself clear?"
Flash gave another terrified nod, and Tony released him, giving him a look of disgust as the teenager scrambled to his feet, blood still running from his nose.
No one would look at him.
With one last whimper, he turned and fled.
Tony wiped his hand across the leg of his suit, and turned to MJ and Ned. "You two are staying here for a while. I already called your parents. Peter left something for each of you."
He spun on his heel, addressing Mr Harrison. "I'm keeping these two. I have parental permission. Tour's over."
Their teacher nodded quickly. "Of course sir."
His eyes went to MJ, and he winked. "Nice punch Michelle."
-------------
Tony took them to the penthouse, showing each of them to a room, and directing Friday to show them the videos Peter had left for them.
Ned came back out openly crying.
MJ was more composed, but there were silent tears streaming down her face.
They sat on the couch beside Tony, where he was staring at a photo in his hand.
It was him and Peter, holding the certificate that Pepper had made to throw suspicion off Tony spending time with Peter, so the media wouldn't know about him.
The two were smiling, and giving each other bunny ears, holding the certificate upside down.
The inane detail made MJ laugh through her tears.
"We're going to get them back," Tony said quietly. "And Thanos is going to rue the day he was born."