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Disclaimer: I do not own Naruto, Naruto Shippuden, Marvel, Agents of S.H.I.E.L.D., or DC. The only thing that I own is my own ideas.

"Talking"

"Super hearing"

"Phone, Intercom, or radio talking"

Jutsu, Abilities, and Powers

(Location) = Scene Break/Time Skip


"Talk. Tell us where you rerouted the plane." Coulson ordered as he made his way down the stairs

"I didn't set this new course. I swear!" May pleaded

"She didn't Coulson calm down." Naruto said trying to deescalate the situation

"The plane just turned around for God's sakes!" Fitz said terrified

"How is this happening then?" Skye asked

"HQ can override automated control of the avionics. Take us anywhere they want. Let me check the instrument panel- and I'll be able to—" May explained before she was interrupted by Fitz

"No way!" Fitz said

"You're not going anywhere till you explain what—" Coulson said

"It's not me!" May pleaded once more

"Why did you have an encrypted hardline to Director Fury?" Coulson asked

"And tried to shoot me when we found it!" Fitz asked/exclaimed

"Let's take a breath…" May suggested

"I agree." Naruto said

"I can't tell you anymore. Director Fury's orders." May stated

"Oh, just come out with it." Fitz said

"That's all you can tell us?" Coulson asked

"I'm under orders." May answered "Fury will tell you."

"What, was this an order? To shoot me in the bloody head?" Fitz asked

"Hold on. We're not headed to Fury anymore." Coulson stated/asked rhetorically

"I don't know where we're headed. And I can't get Fury on the line because Fitz cut the line." May answered

"Skye told me to." Fitz stated before Naruto turned to him

"You're telling me that a level 5 agent took orders from a level 1? I fail to see how that works." Naruto asked only getting a shrug in return

"Someone was talking to The Clairvoyant, the real Clairvoyant." Skye stated

"You were in the walls, Fitz. You wanna explain why you were tampering with the plane's sat cables?" May asked

"Sure, because that's relevant. Don't try and turn this around on me!" Fitz shot back before Coulson look at him

"Fitz has a valid reason." Naruto stated

"Fitz…" Coulson asked

"I was trying to speak to Simmons at the Hub." Fitz explained

"You needed an encrypted line? What's so secret that—" Coulson asked before he was cut off

"You tell me! Simmons and I know you two have been whispering, keeping things from us about the drug that saved your life. Simmons is just trying to figure out how the whole thing works!" Fitz answered/explained causing May to adopt a worried face

"Fitz, who is she talking to?" May asked but received no answer causing Coulson to walk up to the sliding glass doors

"Fitz, open the doors." Coulson ordered

"No way. Not until we sort this out. I'm not opening anything." Fitz said

"Open the door." Coulson ordered once again "We can't get anything sorted until you open the damn door." Before he turned his attention to Skye "Skye, get your laptop hooked up to our systems. See if you can pull up any S.H.I.E.L.D. communications. I wanna know where this plane is headed, and why." Skye then walked up to the sliding glass door and motioned for Fitz to open the door so she could get her laptop and hook it up before Coulson turned his attention to Fitz once again "Now tell me who Simmons is talking to. 'Cause if it isn't someone we trust she is in serious danger."


(Several minutes later – Lab)

Skye had set up her laptop and hooked it up to the Bus just as Coulson ordered as was looking for any S.H.I.E.L.D. communications but all she was getting was distorted radio chatter. Naruto had decided to put himself between May and the rest of the team as to avoid any more conflict.

"All I'm getting is noise." Skye announced

"What do you mean 'noise'?" Coulson asked

"I mean literally, noise. Across every S.H.I.E.L.D. communication channel. Some sort of blanket signal." Skye answered

"Encoded data, maybe?" Fitz suggested

"I think so." Skye responded before Coulson turned to May

"You want to fill us in?" Coulson asked "We root you out, a mole, suddenly our plane shuts down, our communications jammed."

"I don't know what's happening, I wish I did." May stated

"I think I know what's happening." Naruto interjected causing everyone to turn to him

"What's happening?" Coulson asked knowing that Naruto more than likely knew what was going on

"The collapse of S.H.I.E.L.D., Hydra is rising from within." Naruto answered causing everyone to freeze

"And how could you possibly know this unless you are part of Hydra?" Skye and Fitz asked

"Coulson knows how I know but will not say anything without my approval. I will reveal it at a later date." Naruto answered before everyone turned to Coulson

"Level 10 secret sorry." Coulson stated

"If S.H.I.E.L.D. is collapsing why does clearance level matter?" Fitz and Skye asked

"Because we can still salvage S.H.I.E.L.D.." Coulson answered before they heard something

"Do you read, 616?" Garrett called out

"Where is that coming from?" Fitz asked before Skye began typing away

"Close." Skye answered

"Enemy aircraft on my tail! Over." Garret called out

"Garrett?" Coulson asked

"Coulson, I'm under attack. Drones. Repeat. S.H.I.E.L.D. drones are on my ass. We're not getting along. Do you copy?" Garret said

"Copy. Garret, what's happening? We've lost control of our aircraft." Coulson asked

"Hell if I know. Tell me you got guns on that thing. I'm coming to you!" Garret answered

"We got something even better." Coulson stated before he turned to May "See if you can't get back control over the plane." Only getting a nod from May in returned as she walked out of the Lab and up the stairs heading for the cockpit before he turned to Naruto "Can you take care of the drones when they get in range?" Naruto nodded in return before Coulson turned his attention to Skye "Skye, decode the signal. We need to get ahead of this. I don't want any more surprises today."


(Minutes later)

"Garrett, what's your 20?" Coulson asked

"I'll be on top of you in seconds. At your 10 o'clock." Garrett answered "Guns hot?" before Coulson looked to Naruto who only nodded

"Something like that." Coulson answered, seconds later Naruto phased through the plane and took off flying toward Garrett

"What the hell is that?" Garrett asked as Naruto closed the distance quickly

"That would be something even better than our weapons system." Coulson answered as Naruto's eye began to glow red before seconds later twin beams shot out of his eyes destroying one of the drones before destroying the other one

"Coulson what the hell was that?" Garrett asked

"Your rescue. Be grateful." Naruto answered before he flew back to the Bus and phased into it

Seconds later Garrett docked his plane on top of the Bus while everyone gathered in the command center to see what Skye had come up with.

"It's a simple message repeated, semantic encoding. I needed to find the mnemonic key. It should only take me a minute more to decipher." Skye stated as they all looked at the screen and Garrett came down the stairs and walked into the command center

"Can I ask the obvious question? What the hell was that that you sent to destroy the drones? And also what the hell?" Garrett asked

"That would be me." Naruto answered causing Garrett to turn his attention to Naruto

"Son, what you did should be labeled as impossible without anything short of an Ironman suit." Garrett stated

"Yeah, well consider me the impossible." Naruto responded

"Coulson, what the hell is going on?" Garrett asked confused

"We don't know. We don't even know where our plane is headed." Coulson answered

"Oh, I saw your trajectory. You're being tractor-beamed straight to the Hub. Those drones were launched out of there, for sure." Garrett stated

"Victoria Hand." Coulson deduced

"Hand? It can't be." Fitz stated

"Can't be what now?" Garrett asked

"The Clairvoyant." Skye answered causing Garrett to adopted a shocked face

"I thought Ward capped that guy." Garrett said

"I don't believe the man Ward killed was the Clairvoyant. I think he was an unwitting decoy meant to end our investigation." Coulson responded

"That's a lot of trouble to go through for a red herring, don't you think?" Garrett asked

"Because the Clairvoyant is a S.H.I.E.L.D. Agent." Coulson stated "Using high-level clearance to stay ahead of us, make it seem like she's got psychic abilities."

"She? You think Victoria Hand's the Clairvoyant?" Garret asked only getting a nod in return causing him to scoff "I don't mean to pee in the punch bowl, but that doesn't make a lot of sense. I was stationed with Vic in Lisbon. She's a hard-ass and a buzzkill at parties, I grant you, but you really think she's capable of that?"

"Excuse me, didn't she just try to blow you out of the sky?" Coulson asked

"Don't get me wrong, she's definitely gone nuts, but her actions prove she's not The Clairvoyant, right? I mean, if she's been hiding in plain sight all this time, why reveal herself now?" Garret asked as May walked in

"I can't get back control of the plane." May stated

"Guys…" Skye interjected turning their attention to the screen revealing the decoded message

"'Out of the shadows, into the light.'" Coulson read before a new set of letters began decoding

"Well, I'll be…" Garrett said as the letters finished decoding reading 'HYDRA'

"I thought HYDRA was defeated after World War II." Fitz said confused

"It was. S.H.I.E.L.D. was founded in the wake of that victory." Coulson responded

"And now they're back?" Fitz asked

"HYDRA always comes back." Garrett answered

"Cut off a head, and two more will take its place." Coulson added causing Garrett to adopt a thinking face

"Is it a head? I thought it was a limb." Garrett asked

"No, no." Fitz said

"Cut off a limb." Garret said

"It's a head." Coulson countered

"But it was sent from a S.H.I.E.L.D. source. It's got to be some sort of activation signal to HYDRA members within S.H.I.E.L.D." Skye stated

"Hand must be one of them." Coulson deduced "Just like Maelstrom said S.H.I.E.L.D. is collapsing, HYDRA is rising from within." Getting Garrett's attention as he drew his weapon and aimed it at Naruto who wasn't phased in the slightest

"Garrett, what the hell are you doing?" Coulson shouted

"How do we know that Maelstrom isn't part of HYDRA?" Garrett answered with another question

"It's a level 10 clearance secret. Now put the gun away you look like an idiot to everyone." Naruto answered

"Ok, stop, stop." Fitz demanded getting everyone's attention "What does that mean? In S.H.I.E.L.D.?"

"Targeting level 8 agents, seizing power. Wonder how deep it goes." Garrett answered

"This signal is everywhere. Deep." Skye added

"You know what this means?" Coulson asked

"Yeah, we're screwed." Garrett answered

"And we can't change course. And we have no idea what's waiting for us at the Hub." Coulson stated getting Fitz's attention

"The Hub." Fitz said realizing that Simmons was still at the Hub

"I say we blow a hole in the side of this puppy and parachute out. Live to fight another day." Garrett suggested only for Coulson to shake his head

"We can't." Coulson stated

"It's a cherry ride, I'll give you that, but let's not just hand over the keys." Garrett said

"Simmons is at the Hub. We have to save her." Fitz pointed out

"We've gotta save her." Skye agreed

"Oh, crap, yeah. Trip's there, too." Garrett added "I don't mind saying, I don't like the odds on this one. We should let your specialist out of their cage. We can use every weapon we can get." Only for Coulson to shake his head

"People aren't property or object." Naruto snarled even though he didn't like or trust Ward

"No need, Maelstrom is more than enough." Coulson said shooting down the idea

"And why do you say that?" Garrett asked

"You don't even know half of it." Coulson answered cryptically

"Maelstrom is more than enough." Fitz and Skye added

"Well, we can't just leave Ward on the plane when we go in." Garrett pointed out

"That much I can agree on." Naruto said before he turned to Coulson "Go ahead and let him out of the Cage." Coulson then nodded before he walked over to the door to the Cage and opened it getting Ward's attention

"You are being released." Coulson said as Ward got up and walked out joined the rest of the team with Coulson

"So, we'll fly in there, face the music. Even if it is the HYDRA theme song." Coulsons explained

"On the bright side, I don't hear her calling out or screaming my name." Naruto pointed out getting Garrett and Ward's attention

"How the hell would you be able to hear her when we are miles away?" Garret and Ward asked only for Naruto to shake his head

"I can't believe you have not learned yet Ward? You know I'm not going to answer that question." Naruto answered before he turned to Fitz "See if you can't repair May's direct line."


(Minutes later)

Fitz had repaired May's direct line and May was now in the cockpit calling Fury as they landed. As soon as the plane landed Naruto scanned outside with his X-ray Vision to see what was awaiting them, not that he felt frightened only to see several S.H.I.E.L.D. SWAT squads approaching the plane weapons drawn just as May opened the door to the cockpit.

"Fury is dead." May announced

"EVERYONE TO ME NOW!" Naruto ordered as he expanded his magnetic field just as Coulson, Fitz, Skye, Ward, and May ran to him

"What why?" Garrett asked just as the SWAT squads began firing at the plane causing Garrett to drop to the ground to avoid the bullets before he crawled over to the still-standing group that Naruto had made only to see bullets around them frozen inches from everyone as they continued to add up "What the hell?" before he got up and joined everyone else "How the hell are you doing this?

"I passively generate my own magnetic field I merely expanded it to encompass a larger area around me." Naruto answered "Now how are we getting out of here exactly?"

"Well we can't use the cargo ramp, they will be waiting for us." Fitz said "But I can disable the hydraulics to buy us some more time."

"Alright everyone let's go down to the first level to get away from the gunfire." Naruto said before he started moving towards the stairs to the first level as everyone followed after him, as soon as they reached the stairs Naruto retracted his magnetic field and moved the bullets to one side molding them all into one big ball of metal.

They made their way down the stairs and Fitz and Skye immediately headed for the ammunitions and guns locker as Skye pulled down a big duffle bag which the both of them began loading, as Coulson grabbed May and pulled her aside.

"Can that be true? About Fury?" Ward asked

"Man was my S.O., Coulson's, too. Proved himself more than once to be a hard man to kill." Garrett answered as they heard the gunfire continue

"That sound outside doesn't bode well, though." Garrett commented before walking back Fitz and Skye "Is there anything on this plane you don't want them to get their hands on?"


(A few minutes later)

The gunfire had finally stopped, Fitz and Skye had just about got all that they could carry in the duffle bags and Fitz had cut the hydraulics on the cargo ramp. Skye was now backing up the digital contents of the Bus to a S.H.I.E.L.D. hard drive while Garrett set up traps. After that was done Fitz used his 'Mouse Hole' to carve a hole in the bottom of the plane for them to exit through. Now they were trying to find Simmons as they made their way through the halls, weapons drawn.

"It's called a Mouse Hole. Cuts through anything really. I designed it a year ago and submitted it for testing. But it never reached distribution." Fitz explained

"Top agents always hog the good stuff." Garrett commented causing Skye to realize that their hard drive wasn't that safe in her hands and she quickly handed it to Naruto

"You're right, the hard drive's safer in your hands." Skye said "You haven't taught me how to hold up under torture yet."

"I'm not carrying it, give it to Ward." Naruto responded before Skye handed the hard drive to Ward "And we'll get to that." As they came up to a junction

"All right, here's where we split. Skye and Ward…" Coulson ordered before he was cut off by Ward

"Heading to the Nerve Center." Ward said

"Disable their systems, most importantly their control of our plane." Coulson continued

"Copy that." Skye said

"Remember, these agents are under orders. Use ICERs only. We'll find Simmons, get her out." Coulson said as Garrett, Naruto, Fitz, May, and Garrett pushed forward

"We should go straight for Hand. HYDRA's always talking about getting their heads cut off, right?" Garret asked

"Saving Simmons and Triplett, that's our priority." Coulson answered

"I agree, and that's how I'd get it done. Hope you have a better plan." Garrett said as they pushed forward


(A few minutes later)

Naruto, May, Coulson, Garrett, and Fitz had finally reached the security operations room and they had decided to let Naruto lead. Naruto unlocked the door mentally and opened it revealing 3 men, 2 sitting at monitors and a third looking at the door with his rifle. Fitz, Coulson, May, and Garrett immediately shot them with ICERs knocking them out.

"OK, come on, Simmons. Where are you?" Fitz said as he sat down in front of the monitors

"Maelstrom, Hand thinks that Coulson and you guys are HYDRA." Naruto heard Simmons say

"Hand thinks that Coulson is HYDRA." Naruto announced

"But I thought that Hand was HYDRA?" Coulson asked only for Naruto to shrug his arms


(Minutes later)

May was watching the monitors as they cycled through cameras when suddenly it switched.

"There's Hand. Outside the East Wing Situation Room." May announced

"This is definitely a situation." Garrett commented as Fitz walked up to the terminal

"Simmons… We don't move until we find Simmons." Fitz stated

"I'll say it again, the best bet to save her. Use the ventilation system to get above the Sit Room. Drop down using Fitz's sweet little Mouse Hole and put two bullets through Victoria Hand's heart." Garrett suggested

"It's definitely an option, sir." Fitz responded

"Without questioning?" Coulson asked

"Questioning what? Whether she wants to kill us fast or slow?" Garrett asked

"Last time we did that, we shot the wrong man." Coulson stated

"Because she wanted us to. Phil, this is a battle for S.H.I.E.L.D.'s soul, and we're on the front lines. History will remember us this day." Garrett pleaded

"That's right. It's for S.H.I.E.L.D.'s soul. And murder without consideration is a—" Coulson said

"Consideration? Consider this!" Garret responded "She had one of my men killed with a bomb rigged to his gas pedal. The other two were floating in the hotel pool, and they weren't doing the backstroke."

"But we can just as easily ICE her." May interjected attracting Garrett's attention

"You don't put someone like her on ice." Garret responded before he turned his attention back to Coulson "She had Skye shot in the stomach. In the stomach, because she was curious. Mike Peterson burned alive and turned into some kind of freak. She tortured you using the same machine she used to brainwash that bitch in the flower dress." Before Coulson started to adopt an Epiphony type look "And right now, she's probably doing the same to Agent Simmons. Oh, I've considered it plenty, my friend."

"No, Simmons will be fine/Nah, Simmons is just fine." Fitz-Naruto said

"I never mentioned that." Coulson said

"I'm telling you killing her quick would be a mercy." Garrett said

"I never said Raina had been inside the machine. I never told that to anybody." Coulson said

"I must've read it in a report, then." Garrett responded

"You weren't with us." Coulson continued

"The point is, how many more have to suffer before Vic gets hers?" Garrett asked

"You showed up right after." Coulson continued

"What are you driving at?" Garrett asked

"After Skye was shot, Quinn said it was so I would lead the Clairvoyant to the cure. That's exactly what I did. I walked you right in there with me." Coulson continued as Garrett started to panic slightly as he chuckled

"Phil, look, it's been a rough day, I get it. But you need to take a second and…" Garrett said before he paused and sighed before clicking his tongue and shook his head as Coulson made his way over to Naruto "Damn it." Before the doors burst open revealing a squad of S.H.I.E.L.D. SWAT

"Freeze! Don't move." One of them said

"Hands where I can see them." Another one said as everyone raised their hands

"Easy fellas." Garrett said

"Take Agent Garrett into custody! He's the murderer they call the Clairvoyant. He's a traitor!" Coulson said

"Gentlemen. I know Agent Sitwell was in charge of filling your ranks, so at least a few of you know what to do in this situation." Garrett said as the SWAT members just stood there "Anytime, boys." Before a few seconds later 4 of them shot the rest of their members dead, shocking May, Coulson, and Fitz only for Coulson to turn to Garrett who just shrugged his shoulders "Hail HYDRA."

"Hail HYDRA!" the 4 men said as they saluted before going back to keeping the members of Coulson at gunpoint before Garrett put his hands down and walked in front of the 4 men

"Those three men in your unit? Guess they asked the wrong questions?" Coulson deduced

"Until today, it was all about keeping the secret." Garrett answered

"Are you gonna kill us?" Fitz asked

"Fitz you know I won't let that happen." Naruto stated

"That wasn't my plan, really. If it was, I could've done that any time I wanted." Garrett answered "No, Coulson and I go way back. Back to the days when Fury was teaching us tactics." Only to receive a death glare from Coulson "Clearing corners. Slicing the pie. Remember, Phil?"

"Fury would bury you for this." Coulson spat causing Garrett to sigh

"Probably. Instead, he'll just have to roll over in his grave. He must've uncovered our secret. Top brass did what they had to do. Explains why we've suddenly 'come out of the shadows.'." Garrett explained "Not a minor inconvenience, I might add."

"Top brass?" May asked confused drawing Garrett's attention

"Oh my, yes. Tip-top." Garrett answered as he paced back and forth "We had a good thing going, too. Waving the S.H.I.E.L.D. flag as hard as we could. I guess we'll be changing colors now."

"He means Alexander Pierce." Naruto added before Garret turned his attention to Naruto

"I never could get into your file Maelstrom. Not even my top tech guys could. Hell not even Secretary Pierce could." Garrett said

"That would be the unbeatable encryption that I put on it." Naruto retorted

"That's quite the encryption that you put on it." Garrett complemented

"All of this for HYDRA? Do you really believe all that crap? Spreading death and destruction?" Coulson asked

"I wouldn't say I'm a true believer." Garret answered "Let's just say, I felt the wind changing direction and swung my sail. You really should, too."

"I would die before serving HYDRA, you sick son of a bitch." Coulson spat causing Garrett to sigh and click his tongue

"I hate to tell you, but… you've been serving HYDRA all along. I guess death is the only alternative. It's a sad thing. I consider you a friend. I was happy when I heard you'd made it through." Garrett said

"So happy you had me tortured for three days to find out how they did it." Coulson responded

"I didn't enjoy that." Garrett said "Phil, this is me being honest."

"No, John, this is you being a psychopath." Coulson replied causing Garrett to sigh before he turned his attention to May

"I know you'd follow him to the grave, so…" Garrett taunted before he put on a sad face before turning and walking over to Fitz "As for you, Agent Fitz? You'll hold a very high rank on our tech division, if you volunteer. If not, you'll have no rank and a lot of pain. Of course, either way, your services will be required."

"You're gonna suffer for what you've done." Fitz responded "And I plan on being a very big part of that." Causing Garrett to chuckle

"I like you, kid." Garrett responded before he turned his attention to Naruto and walked over to him "You Agent Maelstrom? You will hold a very high rank as protection to the higher-ranked Agents if you volunteer. If not, you'll have no rank and a lot of pain. Of course, either way, your services will be required." Before Naruto and Fitz started to laugh causing Garrett to look at them funny "What's so funny?"

"It's funny that you think anyone on this team will serve or work for HYDRA, especially me, or that you think I will let anything happen to this team, and what makes you think you can control or intimidate me?" Naruto asked

"You've got guts, I'll give you that. What makes you think you are so invincible?" Garrett answered with another question

"Why don't you try and hurt me, find out for yourself." Naruto answered before Garrett smirked as he pulled out his knife and went to stab Naruto only for his knife to bend as soon as it hit Naruto's torso.

Garrett then pulled out his pistol and shot Naruto in the face 5 times each not doing a single bit of damage before Naruto grabbed Garrett by the throat lifting him up and dangled him in the air before Naruto threw him into a wall as the HYDRA SWAT team opened fire on him

Naruto simply expanded his magnetic field and the bullets stopped about 3 inches from everyone before Coulson, and May disarmed the 4 HYDRA SWAT members moments before the doors burst open to reveal Hand, and Simmons along with several men.

"Hands up! Don't move!" One of the men called out as Simmons made a beeline straight for her boyfriend giving him a kiss that he gladly returned

"I'm not HYDRA." Coulson stated hands halfway in the sky

"We heard. Everything." Hand responded as one of the men pulled out what looked like a listening device

"Who is? How deep does it go?" Coulson asked only for Hand to give Coulson silence as his answer


(Minutes later)

Hand and the rest of the actual S.H.I.E.L.D. Agents rounded up all the HYDRA that they had rooted out. Coulson, Fitz, Simmons, May, and Naruto were in a junction when Ward and Skye walked up as Garrett was escorted away as Triplett screamed at him while Coulson broke the news to Ward, who seemed shocked. Afterward, Naruto, Skye, Fitz, Simmons, May, and Coulson regrouped at the Bus where Coulson changed his clothes before he joined the rest of his team.

"Skye, try to restore some of the firmware in the plane's systems. Fitz-Simmons, get a crew together, help May patch the holes." Coulson ordered before everyone but Naruto and May dispersed

"You still want me on board?" May asked confused/hopeful causing Coulson to turn to her

"You're not a friend. But I do believe you're an ally. We need all the allies we can get." Coulson answered

"What are we planning to do next?" May asked

"Survive." Coulson answered as he walked away


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