A/N: I will be referring to Naruto's blood clone that he left at home as Naruto because they are essentially the same person minus the whole 9 biju in his gut.
Disclaimer: I own nothing except for my ideas, meaning I don't own Naruto, DC, or Marvel
'Normal thinking'
"Phone/intercom call/Radio"
"Super Hearing"
"Normal Talking"
Jutsu/Technique/Ability
(Location) = Scene Break/Time Skip
(A few months later)
Naruto and Sakura had been teaching Scampi and Rose how to unlock their chakra as well as watching to see what powers they had inherited from Naruto while the original Naruto was with Coulson and his team in S.H.I.E.L.D.. From what Sakura had witnessed it seemed that Scampi had inherited their Super strength, Naruto's Vibrokinesis, Naruto's Technopathy minus the genius-level intellect that Rose seemed to have inherited, as well as Superspeed through the use of the Speed Force while Rose seemed to have also inherited their Super strength, Naruto's heat vision, Super speed through the use of the Speed Force, they both also seemed to inherit Naruto's invulnerability.
Soon they would be starting preschool alongside Morgan, which Sakura was worried about because she was worried that they would awaken and therefore display any latent abilities or powers that she hadn't caught yet, and in turn, they would be labeled as freaks and isolated or kicked out of preschool. She was also worried that if they did awaken and accidentally display latent powers then the government or some organization would step in and try and take them from her while she wasn't there, to try and ease her worries she told them that if they ever were in serious trouble to scream out Naruto's name to let him know so that they could step in.
From what they had heard from Steve Rogers, Peggy had begun going on missions with him now that she was his equal in strength. Steve had asked Naruto if there was anything that he could do in terms of protection for Peggy, Naruto in turn asked Steve to bring his Shield in for Naruto to take a look at to see if he could make anything similar. As requested Steve brought his Shield to Naruto who used his Microscopic Vision to examine the molecular structure of the shield and in turn use his Creation of all things technique to create a duplicate of Steve's shield for Peggy to use.
S.H.I.E.L.D. had a ton of questions pertaining to what exactly happened to Peggy as well as how she got her own shield that was exactly like Steve's, as Naruto instructed she said that she underwent several experimental surgeries and that Steve had gone to someone special to make her a shield, but that didn't stop S.H.I.E.L.D. from doing their own investigation. S.H.I.E.L.D. had backtracked Peggy's steps as far as they could but that only lead them to find that Steve had signed her out of her nursing home himself and taken her somewhere, where that was they couldn't figure out.
Naruto and Sakura were teaching Scampi and Rose how to unlock their chakra when Naruto heard someone call out to him
"Naruto we may need your assistance if you're willing to offer your help. We're in Washington D.C.." Naruto heard Fury say before he got up and turned to Sakura
"It seems that Fury and others may need my assistance. I'll be back as soon as I can." Naruto said before he gave Sakura a kiss and opened a portal to Washington D.C. and stepped thru before he took off a few seconds to search for Fury's chakra signature, once he had a lock he took off running.
(A few seconds later – S.H.I.E.L.D. Dam Facility)
Naruto came running in as a trail of orange lightning surprising Natasha, Steve, Peggy, and a black man with brown eyes wearing a swamp green t-shirt that kind of hugged his form.
"You called." Naruto said before he took in Fury's current state "What the hell happened to you?" before he turned to the black man "And who's this?"
"Names Sam Wilson. Who are you?" the now-named Sam Wilson answered
"Names Naruto Uzumaki, I'm the one that Fury called out to." Naruto answered before he turned to Fury waiting for an answer
"S.H.I.E.L.D. has been compromised, HYDRA within S.H.I.E.L.D. came for me. Left me with a lacerated spinal column, a cracked sternum, a shattered collarbone, collapsed lung, perforated liver, and one hell of a headache." Fury explained
"We have to stop the launch." Natasha stated before Fury turned to her
"I don't think the Council's accepting my calls anymore." Fury responded
"Launch of what? Does someone mind filling me in?" Naruto asked
"Project Insight." Steve answered before Naruto turned to Fury
"You mind filling me in on what exactly 'Project Insight' is?" Naruto asked
"I'm sure you are aware of the new helicarriers that Tony updated. Well, they are also heavily armed, capable of crossing numerous potential threats off at a time. We started the project as a direct response to the Battle of New York." Fury explained he opened a briefcase holding 3 big chips for everyone to see as Hill opened a laptop and turned it toward everyone
"What's that?" Sam asked
"Once the helicarriers reach 3,000 feet, they'll triangulate with Insight satellites, becoming fully weaponized." Hill explained
"We need to breach those carriers and replace their targeting blades with our own." Fury added
"One or two won't cut it. We need to link all three carriers for this to work because if even one of those ships remains operational, a whole lot of people are gonna die." Hill continued
"We have to assume everyone aboard those carriers is HYDRA. We have to get past them and insert these targeting blades. And maybe, just maybe we can salvage what's left…" Fury added
"We're not salvaging anything. We're not just taking down the carriers, Nick. We're taking down S.H.I.E.L.D." Steve barked
"S.H.I.E.L.D. had nothing to do with this." Fury barked back
"You gave me this mission. This is how it ends. S.H.I.E.L.D.'s been compromised. You said so yourself. HYDRA grew right under your nose and nobody noticed." Steve said standing his ground
"Why do you think we're meeting here? I noticed." Fury said
"How many paid the price before you did?" Steve asked
"Steve, honey, calm down." Peggy said
"Look, I didn't know about Barnes." Fury said
"Even if you had, would you have told me?" Steve asked "Or would you have compartmentalized that, too? S.H.I.E.L.D., HYDRA, it all goes."
"He's right. I think it's time to pass the torch." Hill agreed before Fury looked around the room
"Well, Captain, looks like you're the one giving the orders now." Fury said
"I hate to but in but can't you just call in that one Avenger that sent that purple ball through the portal back in New York that took care of the Chitauri? I'm sure he could take care of this easily." Sam asked
"Our deal was that anything not of this planet that showed up he would deal with. Although, I guess I could ask him considering he's in this room with us." Fury answered before he turned to Naruto "Would you mind lending a hand in saving millions of lives?"
"I wouldn't be here if I wasn't willing to lend a hand." Naruto answered
"I need to go clear my head." Steve said before he walked off as Peggy followed him
(Half an hour later)
Steve had cleared his head and came back down and was now ready to go take down Project Insight. Natasha had hacked into S.H.I.E.L.D. and found out that they were meeting to launch Project Insight.
"Alright so here's the plan. Me, Peggy, and Sam will raid the Helicarriers and switch out the targeting blades with Naruto running backup if any of us need it. Natasha will infiltrate the World Security Council as Pamela Hawley, with her inside she can dump all of S.H.I.E.L.D. and HYDRA's files on the internet for everyone to see." Steve explained
"Do me a favor and delete anything that S.H.I.E.L.D. or HYDRA has on me or my family before you dump all the files onto the internet." Naruto said
"You need two Alpha Level members to disable the encryption." Fury said before Steve turned to him
"Then you can meet Natasha there." Steve said "Alright everyone has their mission, everyone sync up your comms, suit up, and let's head out." Before everyone synced their comms up as Naruto's suit bled onto him before he turned to Sam
"When I am suited up please refer to me as Maelstrom as I wish to remain anonymous should someone hear us." Naruto stated getting a nod from Sam
"Call me Falcon." Sam responded
(2 Hours later – Triskelion)
Steve had gone to the Captain America museum and stolen his war suit, now Steve, Peggy, Sam, Naruto, and Maria Hill were on their way up to communications. When they reached the locked door separating them from the communications room Naruto mentally unlocked it with his Technopathy before they opened it and proceeded through surprising everyone in there, after which they took over the communications center of the Triskelion.
Steve approached the microphone that would broadcast his voice across the entirety of the Triskelion.
"Attention all S.H.I.E.L.D. agents, this is Steve Rogers, or as some of you know me Captain America. You've heard a lot about me over the last few days. Some of you were even ordered to hunt me down. But I think it's time you know the truth." Steve announced before he paused for a second "S.H.I.E.L.D. is not what we thought it was. It's been taken over by HYDRA. Alexander Pierce is their leader. The S.T.R.I.K.E. and Insight crew are HYDRA as well. I don't know how many more, but I know they're in the building. They could be standing right next to you. They almost have what they want. Absolute control. They shot Nick Fury. And it won't end there. If you launch those helicarriers today, HYDRA will be able to kill anyone that stands in their way. Unless we stop them. I know I'm asking a lot. But the price of freedom is high. It always has been. And it's a price I'm willing to pay. And if I'm the only one, then so be it. But I'm willing to bet I'm not." Before he backed away from the microphone as Sam walked up
"Did you write that down first, or was that off the top of your head?" Sam asked
"Off the top of my head." Steve answered
(Minutes later)
Steve, Peggy, Sam, and Naruto quickly made their way down to the ground floor after it was revealed that the launch of the helicarriers had been overridden and they had been launched early. They were now running to the slowly rising helicarriers.
"Hey, Cap, how do we know the good guys from the bad guys?" Sam asked
"If they're shooting at you, they're bad." Steve answered as they neared the edge before Sam engaged his flight suit causing wings to deploy before the engine on his back propelled him forward heading for the highest helicarrier as Steve jumped down to the slowly rising helicarrier beneath him, Peggy then looked at the last helicarrier which was out of her reach before she turned to Naruto
"Mind giving me a lift love?" Peggy asked before Naruto smiled and grabbed onto Peggy's collar before he took off flying towards the last helicarrier
After Naruto dropped Peggy off he saw Sam evading fire from some pretty big guns on the helicarrier he was trying to get into. Seeing that Sam needed help Naruto took off flying towards him.
"Hey, Cap, I found those bad guys you were talking about." Sam announced
"You okay?" Steve asked as Sam continued to evade gunfire
"I'm not dead yet but I could use some backup. Maelstrom, any help would be much appreciated." Sam answered
"On my way now should be there in a couple of seconds." Naruto announced as he closed in before twin beams of red energy shot out of Naruto's eyes destroying one of the guns firing at Sam causing all the guns to turn their attention to Naruto "I got their attention, do you need a way in?"
"If you wouldn't mind that would be great." Sam responded before twin beams of red energy shot out of Naruto's eyes once again carving a hole in the bottom of the glass dome on the bottom of the helicarrier big enough for Sam to fly in
"There you go." Naruto said
"Thank you very much." Sam responded before he flew threw the hole "I'm in. Bravo lock." Before he jumped out of the hole that Naruto made for him and took off flying
"Falcon now that your targeting blade is in place why don't you back out and go back to Hill. I've got it from here." Naruto suggested only getting a nod in return before he headed back to the communications tower
"Cap, Peggy, where are you at?" Maria asked
"Working on it." Steve answered
"Same here." Peggy answered
(Several Minutes later)
"Alpha lock." Steve announced "A pickup would be nice Maelstrom." Before Naruto took off towards Steve's helicarrier, a couple seconds later he phased threw and grabbed Cap
"Steve honey, Maelstrom, I have an unexpected guest that is preventing me from delivering the last targeting blade. Help would very much be appreciated." Peggy announced and with that Naruto phased them both out the bottom of the helicarrier and darted off towards Peggy's helicarrier
A minute later Naruto and Steve arrived to find Peggy and Bucky Barnes fighting on one of the bridges suspended, Naruto dropped Steve off behind Peggy so that Steve could switch places fighting Bucky and allow Peggy to deposit the last targeting blade.
"Charlie lock." Peggy announced before she turned around "Steve, Honey, lets get out of here before Hill hits the fire button."
"I'm not leaving until I get through to Bucky." Steve responded
"Helicarriers have reached 3,000 feet, triangulating with Insight satellites now. Get out of there." Maria Hill announced before Steve kicked Bucky back and turned to Naruto
"Will I have other chances?" Steve asked only getting a nod in return before he turned back to Bucky
"You know me." Steve said before Bucky tried to punch him
"No, I don't!" Bucky shouted
"Bucky." Steve called out "You've known me your whole life." Before Bucky tried to punch him again "Your name is James Buchanan Barnes."
"Shut up!" Bucky shouted before he rushed Steve only to get kicked back
"I'm not gonna fight you." Steve said before he dropped his stance "You're my friend. And I will come for you. Not this you, but the you that is my best friend. Because I'm with you to the end of the line." Before he turned around and walked over to Naruto and Peggy as Naruto opened a portal to the ground and sent Bucky flying threw it with a wordless Almighty Push before he opened a portal back to Maria that everyone else stepped thru.
(Communications Tower)
A portal opened behind Maria Hill before Naruto, Peggy, and Steve stepped thru just as Maria Hill the fire button, all the helicarriers took aim at one another and started firing.
"Well now that the helicarriers are taken care of I do not believe you need my help anymore, is that correct?" Naruto asked
"I believe that to be correct, we only enlisted your help in being backup for taking down the helicarriers, seeing as they are now neutralized I do not believe your services are required anymore." Maria answered before Naruto turned to Steve and Peggy
"Well, you guys know where to find me and how to get in contact with me should you need it in the future, and with that I will now be taking my leave." Naruto said before his suit flowed back into his necklace as he opened a portal back home and stepped thru it as it closed behind him
(Uzumaki Residence)
A portal opened in the living room before Naruto stepped out as it closed behind him revealing Sakura, Scampi, and Rose whose attention was diverted to Naruto.
"S.H.I.E.L.D. has fallen and is no more. Fury asked me to run back up while they took down those helicarriers that Fury consulted Tony on." Naruto announced "Now let's get back to teaching our kids."
(The next day)
After the aftermath and official fall of S.H.I.E.L.D. Maria Hill immediately joined Stark Industries to protect herself from legal prosecution as well as became Tony's second in command.
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