I took down the original story, because I had a second thought about what I'm doing with it, so I changed a few and got an actual plot.

(AoS doesn't happen in this universe)

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Washington, D.C., the Triskelion. Inside Fury's office, he's being told there might be a organization hiding inside S.H.I.E.L.D. by his two closest friends and head scientists, Richard and Mary Parker. "Are you sure about this, Richard?" Fury asks. "If we throw something like this into the wind, we could turn everyone on each other. And put a target on your heads." Fury explains. "We know how it seems, Nick, that's why we're asking for permission to fly to the Hub, to see what we can find. And that's why I'm hoping only we can know about this." Richard asks. "And what about if they found about Peter's...abilities?" He asks, regarding their kid who gained powers after one of their spider experiments got to him. "We hope they don't come forward for years, but we're doing this so nobody learns, except for S.H.I.E.L.D." Richard explains. Fury thinks for a second and sits down. "You're on a thin leash, Richard. See what you can find." He says. "Thanks, Nick." Richard says and they leave his office.

"What about Peter? We can't just take him to the Hub." Mary says. "Maybe we can ask Coulson to babysit for a few days. We know he loves kids." Richard says. "You sure he's not doing anything?" She asks him. "If not, what's he gonna say? "No, I've got nothing to do, and I love the kid"?" He asks. "We'll see, wont we?" Mary says as they walk to Coulson's office. Inside Phil's office, "only for a few days?" Coulson asks. "Yeah, that's all we ask. Fury's sending us to the Hub and we can't take Peter with us." Richard explains. "Sure, I guess I can watch him. I can ask Fury for a few free days and I can watch him." Coulson says. "We can't thank you enough, Phil." Mary says. "Come on, I love the kid. Leave it to you two to create a bundle of joy." Coulson says, chuckling.

Few days later, they're on an private plane 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 asks. "He's the first enhanced human since Captain America." She keeps saying. "Coulson will protect him." Richard tells her. "He'll always be protected." She starts calming down. "I'll be back." Mary says as she goes to the bathroom as Richard keeps trying to crack it and the pilot doors open and he steps out. "Mr. Parker." He says and starts washing his hands over the sink. 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." Richard says. "Well, he didn't. Garret did." Ward 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, 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." He 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?" He asks, trying to see how he missed it. "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 says. "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." Rumlow says. "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." He says. "I'd die before I let you turn him into a weapon for HYDRA." 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 wast. Don't worry, we have plenty of people looking for your son. We already checked with your wife's sister. May, is it?" He asks. "What?" Richard asks. "Yeah, she was a nice girl. Sorry to see her go on a robbery gone wrong." Rumlow says, faking empathy. Mary breaks the door open and Ward 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 Ward in the head. Ward turns and shoots her, point blank. "Mary!" Richard shouts as he gets back up and kicks Rumlow unconscious. He grabs the gun and goes to Mary. "Hey, you're okay." He says as he moves her to a seat. "Richard...Peter." Mary gasps. "He's with Coulson. They don't know where he is. He'll protect him." Richard says. "The laptop." She says and Richard sees it on the ground. Richard takes it and goes back to contact Fury. "I gotta let him know...we might not make it back." He explains as Rumlow gets back up and punches him and he falls. Rumlow takes his gun and shoots at the front of the plane and the dead pilot falls forward on the wheel and they start falling in the air as Rumlow takes a parachute and heads for the exit. "Sorry it had to end this way, Richard." Rumlow says. Richard looks over to Mary as she has the laptop and already sent another message to Fury. "It's been an honor to meet you, mrs. Parker. I'm Rumlow, by the way." He says as he leaps out of the jet. They can't do anything as the plane starts to go down and crash into the ocean.

Back in Washington, Coulson gets woken up by a crying infant. He gets up and walks over to the guest room, now the infants room. He opens it and sees him crying. "Hey, Peter, what's wrong?" He asks calmly. "You sound scared." He says as he picks him up. "You miss your mom and dad? Don't worry, they'll be back." He says calmly as his phone goes off and sees it's Fury. He answers it. "Director, what's the situation?" He asks. "Get to my office. Fast. Bring Peter. Don't leave him out of your sights." Fury says and hangs up. "It must be serious if he's willing to put up with a kid." Phil tells Peter. "Either that or he wants to see you." He says, jokingly as they make their way to the Triskelion.

Inside his office, Phil sees Natasha Romanoff and Clint Barton. "What's going on, Fury?" Phil asks, still with the infant. "Coulson, you brought Peter. Good. There's something I need to tell you...the Parker's are dead." He bluntly says. "What?" Phil asks. "They were on their way to the Hub, weren't they?" Phil asks. "The jet crashed. They never made it. The signal went dead and we can't find the wreckage. But before the signal went dead, we received a message." He says and turns his screen around and they read the message. "S.H.I.E.L.D. is compromised."It reads. "There's more." He says and shows the latest message. "They're after Peter. Keep him safe." It says. "Who's "they"?" Phil asks. "I don't know, after we received this, the signal went dead. Peter's in trouble from someone who took them out to keep this a secret." Fury explains. "Who's going to look after him?" Phil asks. "I looked into close relatives, and it would seem his only other relative being his aunt and uncle from New York were killed in a robbery gone bad." Fury says, looking out his window. "The entire Parker family is gone. Peter's the last of them." Fury says. "Okay, back to his original question. What do we do with him?" Clint asks. "They left something else in their message, Phil." Fury says and he goes back to the first message. "We trust you, Phil. Take care of him." It reads. "They trust me?" He asks. He looks at the infant in his arms. "I...guess I can't let them down, now can I, squirt?" He asks Peter as he laughs. "He'll need training as he gets older to protect himself. He's still gonna go through some alone time phases, Phil." Fury says. "We can take care of that." Natasha says. Clint looks at her, confused. "Really?" Clint asks. "Why not? You want whoever's after him to get him?" Natasha asks. "I guess not." Clint says. "Thanks, guys." Phil says. "Don't worry, kid. We'll keep you safe. For your parents." Phil says as Peter starts falling asleep again. Natasha walks over to them and Phil expected Peter to start crying as he always does when he gets too close to strangers and he doesn't. "I guess he likes you." Phil says as Natasha puts her hand on his cheek as he sleeps.

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Next chapter is gonna take place during Thor, and will be quite short until moving on.