Richard and Mary were currently on their private S.H.I.E.L.D. plane headed to the Hub.
Richard is trying to hack into a secret server inside the Hub to locate the source.
"What could this code mean?" Mary asks.
"I think it's supposed to be an activation code." Richard says.
"Wait. I think it cracked it." Richard says as part of the code comes through "out — — — in— — light"
"It's just...what if they know?" Mary asks.
"Who know what?" Richard asks.
"What if these people know about his powers?" She explains to her husband. "He's the first enhanced human since Captain America."
"Coulson will protect him." Richard tells her. "He'll always be protected."
She starts calming down and needs to go to the bathroom. "I'll be back." Mary says as she goes to the bathroom whilst Richard keeps trying to crack it and the pilot doors open and he steps out.
"Mr. Parker." He greets and starts washing his hands over the sink while Richard looks and sees something on his hands he sees and thinks it's blood. Richard starts getting suspicious. "No rest for the future, huh?" He asks.
"No, it would seem not, Rumlow." Richard says. "I don't really see why Fury assigned you to this."
"Well, he didn't." Rumlow explains as he turns in the sink. "So, what is it you're working on that's so secret?" He asks.
Richard looks and another part comes in "H— H-D-A" it says, still incomplete. "I'm just...planning ahead." He explains, disturbed. "You don't know what's gonna happen." He explains. So, you think I can radio the Hub and make sure they're prepared for our arrival?" He asks, getting up.
"Step ahead of you. Already done." Rumlow says.
"I think I'd like to make sure for myself." Richard says as Rumlow pulls out a gun.
"I think we both know that's not an option, Doctor." Rumlow says.
Richard looks back at the computer as the message comes clear. "Hail HYDRA" He looks back to Rumlow in shock. "You're HYDRA?" Richard asks. "HYDRA is still around?"
"Oh, don't worry, even the Director is clueless. We've been here since Rodgers tried beating us." Rumlow explains.
"Cut off one head, two more grow back." Richard understands.
"You know, they told me to kill you." Rumlow explains. "Then take whatever you have on us. But I can offer you a chance to see your son again. Garret wants to offer you a choice." Rumlow explains.
"A place in HYDRA?" Richard asks.
"All we want to know is what your son can do. And where we can find him." Rumlow shrugs.
"I'd die before I let you turn him into a weapon for HYDRA." Richard promises him.
Rumlow looks sad. "Come on, Richard, think of your son." Rumlow says.
"I am. That's why I'm not joining." Richard tells him.
"I'm sorry to hear that." He says and walks towards the bathroom door and makes sure it's locked. Richard takes this time to send a message to Fury. "S.H.I.E.L.D. is compromised." It says and sends it as Rumlow turns back around.
Mary tries getting out of the bathroom and is having trouble. "They say you're a genius. S.H.I.E.L.D.'s best to offer." Rumlow says as he takes his laptop. "Sadly, it's a waste. Don't worry, we have plenty of people looking for your son. We already checked with your wife's sister. May, is it?"
"What?" Richard asks.
"Yeah, she was a nice girl. Sorry to see her go on a robbery gone wrong." Rumlow says, faking empathy.
Mary then breaks the door open and Rumlow gets distracted and turns to her. Richard takes the opportunity to punch him, and he stumbles and kicks Richard off of him and aims the gun at him. Mary takes a wine bottle and hits Rumlow over the head, rendering him unconscious.
"Mary!" Richard shouts as he gets back up and kicks Rumlow in the face to make sure he stays unconscious.
"Richard, what's going on?" Mary asks.
"We discovered something big." Richard tells her before going around, searching for rope and tape before wrapping it around Rumlow to keep him from going anywhere.
Once they reached the Hub, Rumlow was arrested for attempted murder of Agents Mary and Richard and the death of May and Ben Parker.
"So, we got Rumlow to confess everything, found out that HYDRA has infiltrated all of S.H.I.E.L.D., and we even discovered that they had James Buckhannon Barnes as some brainwashed hit assassin and now he's going through our reentry program and filling him in on everything he missed." Mary lists everything while she and Richard sat in a booth holding baby Peter at a café with Superman and Batman sitting across one another.
"Well, congratulations you two." Superman cheers. "You guys saved countless lives."
"Yeah, both agent and average people." Batman says. "So, what happens next? Isn't your kid still going to grow up to be, you know, different?"
"Yeah, that kid's going to have some major problems growing up." Superman agreed as he looked at the baby who was just babbling nonsense.
"Well, whatever comes of him and what he can do, we'll be ready to deal with it." Richard promised.
"Yeah...this feels like a letdown." Batman admitted.
"What do you mean? That we're still alive?" Mary asks.
"Yeah, I feel like that and you stopping HYDRA this soon could have some strange repercussions for the future." Batman explains to them.
"Like what? S.H.I.E.L.D. not falling apart? Us being able to raise our kid?" Richard questions. "It sounds perfect to me."
"Yeah, a lot of viewers might disagree." Superman guesses.
"Why?" Richard questioned.
"BECAUSE I'M BATMAN!" Batman suddenly said, confusing them all. "Sorry, it's my thing."
The years go on, and Peter grown up to reveal he in fact does have superpowers but decides to use them on behalf of his fallen family members to become New York's friendly neighborhood superhero.
Whilst that happened, S.H.I.E.L.D. was always there, helping him become a better hero and when the Avengers were formed, Peter helped them to stop Loki.
They helped the fall of Ultron, and the biggest threat of them all Thanos came to kill half of all life, S.H. .D. was there to help keep Thanos and his allies back whilst the residents of Wakanda removed the Mind stone from the Vision.