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I have made an edit to chapter 9 as I missed a key point making the story inconsistent

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

"Talking"

"Mind reading"

"Super Hearing"

"Phone, Intercom, or radio talking"

Jutsu, Abilities and Powers

(Location) = Scene Break/Time Skip


(An hour and a half later – Bus)

As soon as Coulson had been taken they immediately dropped Ace off with a S.H.I.E.L.D. agent that would take him back to Mike's sister, now they were back at the Bus, when suddenly Naruto's phone rang.

"Sir. Nick Fury is calling." Hagoromo said causing everyone to start looking around for the source

"I figured as much." Naruto said

"What was that?" Skye, Fitz, Simmons, and Ward asked

"That would be my personal A.I., I named him Hagoromo." Naruto answered causing Fitz to perk up

"You have a personal A.I.? Who did you buy it off of? Tony Stark?" Fitz and Skye asked

"Noone, made it myself." Naruto answered

"What can your A.I. do?" Fitz and Skye asked

"Anything really." Naruto answered "Anyways I need to take this call. Don't take off without me." Before he walked off to answer his phone

"What's up Fury. Am I to assume this is about Coulson being captured?" Naruto asked

"I put you on that team to make sure nothing happened to Coulson and his team. From what I have heard so far you have done phenomenally up to this point." Fury said "Why exactly did you let them take Coulson?"

"1. If I did anything they would have killed Mike's son 2. I know for a fact that Coulson will not die, he will be alright 3. Certain things have to happen to ensured this timeline stays intact." Naruto answered/explained

"How do you know that he will be alright? Are you part of Centipede?" Fury asked/accused

"I am able to see glimpses of the future and I know for a fact that Coulson will be okay. But he will know part of what happened to him." Naruto explained

"What part will he learn about?" Fury asked

"How long he was really dead and that you altered his memory." Naruto answered

"I guess it's okay so long as we get him back in one piece." Fury said "Alright then carry on." Before he hung up the phone and Naruto began walking back towards the Bus


(35 and a half hours later – Command Center - Bus)

The Bus was now overwhelmed with S.H.I.E.L.D. Agents, currently Agent Hand was debriefing everyone, including Naruto.

"The burned remains recovered at the site are believed to be those of Agent Trainee Michael Peterson. Other physical evidence has proven scarce. Nothing relating to Mr. Po, his Centipede associates, or their location have been found." Hand explained

"Any progress with Vanchat?" Ward asked

"Nothing actionable, Agent Ward. But I have my best interrogator in there right now." Hand answered before he tapped on the touchscreen table and live feed of the Cage "Vanchat will talk, and rest assured, when he does, not a single stone will be left unturned until we take down Centipede."

"And get Coulson back./And find Agent Coulson." Fitz-Simmons said

Just then an alert popped up clearing the screens

"We have a security breach. Someone's hacking the system." Hand announced before May adopted an irritated expression

"No, we aren't, I know who caused this." May said before her, Naruto, Ward, and Hand walked over to Skye's bunk to which Hand opened the door

"Just in time." Skye said before he held up her wrist "Can you override this?"

"What do you think you're doing?" Hand asked

"The money trail's our key to finding Coulson. I just need to gain access to Vanchat's financials, and from there, I should be able to trace Centipede's payments and then hack into their account." Skye explained

"You're the consultant, the one who shot Agent Sitwell." Hand said

"Technically wasn't me." Skye corrected

"I want you off this plane immediately." Hand ordered before she started walking off

"What?" Ward asked before Skye got up from her bed to follow Hand with Naruto, Ward, and May following behind her

"Wait. I know I'm not some bad-ass field agent like May or Ward, but this is what I do. You can't just kick me off this mission." Skye pleaded before Hand turned around to face her "Listen, I'll do whatever you say. All this protocol crap doesn't matter to me. All that matters to me is Coulson."

"Well, all this 'protocol crap' matters to me. You're a distraction. And you're gone." Hand said

"Agent Hand." Ward said causing her to turn around "I know Skye's methods are unorthodox. But she's a member of this team. She can help."

Hand then turned to May "Agent May, your professional opinion. Will this girl be of any use to us on this plane?"

"I need to get Skye off this plane, away from all these Agents." Naruto heard reading May's mind

"No." May answered

"Increase her restriction level, and confiscate her laptop and phone. Then have her delivered to debrief." Hand ordered to another Agent

"Yes, ma'am." The agent said

"Yeah, sorry, not going to happen." Naruto said "You will not be taking anything from her. Or increasing her restriction level."

"Excuse me? And who do you think you are?" Hand asked baffled

"An Agent with Level 10 clearance so that means I outrank you. As I said you will not be taking anything from her." Naruto stated "Look me up if you really want to, Agent Maelstrom."

"Well, regardless I want her off this plane." Hand said

"I can work with that." Naruto agreed before he turned to Skye "I'll escort her out I am her S.O. after all."


(A couple minutes later)

Naruto and Ward who insisted on coming were escorting Skye down to the first level of the Bus when Skye decided to talk as they were coming down the stairs.

"It's clear that May has an ax to grind with me, but that was way out of line." Skye said

"No one knows what's in May's head except May." Ward stated "Don't worry. Coulson will make this right when he gets back."

"I can find him." Skye whispered

"I believe you. I've seen firsthand what you can do even without S.H.I.E.L.D. resources." Ward whispered

"May just wants to get you off this plane. Away from all these Agents." Naruto whispered

"And how do you know that? Did she tell you?" Ward asked

"That's for me to know, and you never to know." Naruto answered before Fitz-Simmons walked up

"Hang on. Hang on." Fitz said as Simmons walked up with a brown paper bag

"We have something for you." Simmons whispered

"You made me a sandwich?" Skye asked confused

"Yes, it is that." Simmons said

"It's a satellite phone. Damper-resistant. You get one shot before your bracelet shuts it down." Fitz whispered

"So only call in case of emergency." Simmons added

"Good luck." Naruto, Ward, Fitz, and Simmons said before they walked off, Naruto and Ward headed upstairs while Fitz-Simmons headed back to their lab


(Half an hour later – Lab)

Naruto was meditating as per usual on a stool off to the side while Fitz-Simmons did their thing and Ward watched the interrogation on the big screen.

"No! That's too much. I know the Sleepy rounds no longer affect the Centipede Soldiers, but all we want to do is disable them, not kill them." Simmons said as one of the techs helping her overfilled a round

"Personally, I'm good with either." Fitz commented causing Simmons to look up at him

"Babe, you don't mean that. Those soldiers are just men…" Simmons started trying to reason with her boyfriend

"Who could smash your skull open with a single punch." Fitz said interrupting Simmons

"But they're being controlled. Making them fight against their will." Simmons said

"Well, they took Coulson. I don't care what we have to do to get him back. We need to bring him home." Fitz said

"And we will Fitz. Just relax Coulson will be okay, he can handle himself." Naruto said

"What's this guy doing? Lulling Vanchat to sleep?" Ward asked causing everyone to look up at him "I'm going in." before he walked off


(A couple minutes later)

Fitz-Simmons were watching the Cage feed when Ward signaled for them to open the top of the cage.

"Rochambeau you." Fitz said before he turned to Simmons

"Rochambeau." They both said with Simmons picking Rock and Fitz Scissors

"Scissors? Oh, Babe!" Simmons said pitying her boyfriend before she tapped a button on her tablet


(Hours later – Lab)

Ward and May were gathered as Fitz-Simmons debriefed them on a new device they made to neutralize Centipede soldiers.

"The Centipede soldiers each have a port on their delivery device to inject refills of serum." Simmons explained

"With this injector cuff, we can use the port to our advantage." Fitz continued

"By injecting a refined dose of dendrotoxin to incapacitate the soldier." Simmons finished

"How does it work?" Ward asked

"Oh. Just simply lock it around the Centipede soldier's forearm." Simmons answered as she locked the mechanism around Ward's wrist

"And night-night superpowers." Fitz commented

"That sounds like riding a bull for 8 seconds." Ward said causing Naruto to laugh

"Yeah, exactly. It's that simple." Fitz stated

"Yeah." Simmons said

"Looks like you got your work cut out for you." Naruto joked causing Ward to turn around to confront him when suddenly Naruto heard Skye's voice

Italics "Maelstrom I'm calling now." Skye said

Naruto looked around to see if the coast was clear when he spotted 3 techs at the holotable "You three out now." They immediately left just as Simmons's phone rang causing Ward to look at Naruto funny

"Hello?" Simmons said

"Simmons. It's me." Skye said

"What did you find Skye?" Simmons asked

"I may have a lead on where Centipede's holding Coulson." Skye answered just as May walked over and took the phone from Simmons

"Skye. What have you found?" May asked before Ward turned to Naruto

"How did you know she was calling?" Ward asked

"Have you genuinely not learned that I am not going to reveal anything you?" Naruto asked

"But if I know what abilities you have we can better senergize." Ward said

"I don't give a shit. I told you that I do not trust you, that fact alone seals the deal on me revealing anything to you." Naruto stated "Now drop it before I put you to sleep again."


(Several Hours later)

Naruto, May, Fitz, Simmons, Ward, and Skye had gathered and were getting ready to follow the lead that Skye gave them just as Hand and an assault squad were prepping for a raid.

"We're about to launch a major assault on a Centipede Lab, and you wanna take your team to the desert based on a hunch from Skye?" Hand asked

"It's not a hunch." Ward answered

"Skye followed the money from Vanchat back to Centipede." Fitz added

"You know the thing that she said she wanted to do prior to you to booting her off this Bus might I add." Naruto added

"Turns out, they recently purchased a small development less than 100 miles from here." Simmons finished

"Well, that's great news for their real estate portfolio. But we have confirmed activity at the lab. I'm taking a strike team to investigate. End of story." Hand stated

"So we split up. You take the strike team and go after Centipede. We'll investigate Skye's lead, see if Coulson's there." May offered

Hand adopted an epiphany-like look "You backed my decision to kick Skye off the plane."

"Seems like it worked out." May responded

"Seems like you played me." Hand stated

"Look, it's nothing personal. But I am taking my team and we're gonna find Coulson. Send back-up if you want." Ward said before walking over to the SUV followed by May, Fitz, Simmons

"I'd like to make it apparent that I did not agree to being part of this team. I'm only going to find Coulson." Naruto stated before he followed after them


(2 hours later – Unknown Location)

Ward and his team had just arrived at the location provided by Skye just in time to incapacitate a Centipede soldier that was chasing Skye with the SUV. Everyone got out and just looked around.

"Coulson's gotta be here somewhere. We need to split up." Skye recommended

"Can't Maelstrom sense him?" Ward asked causing them all to turn to Naruto

Naruto sighed before he began searching for Coulson's chakra signature, being so close he immediately sensed it "He's in the biggest building." before he used his Xray Vision to look inside the building "He's inside some sort of machine, Raina's inside the building with." Just as Simmons looked behind her to see a Centipede soldier

"Or run." Simmons suggested

"Alright Ward, looks like your up." Naruto stated before Ward pulled out the injector cuff that Fitz-Simmons made

"I got him." Ward said

"Are you sure?" May asked before Ward looked at the injector

"I got this." Ward said before he started sprinting at the Centipede soldier

"Come on let's go get Coulson." May said before they started running toward the biggest building

As soon as they entered the building Raina got up "It's for his own good." Before Skye went up and knocked her out before running over to Coulson

"Please let me die! Please let me die!" Coulson whimpered before Skye started trying to turn the Machine off "Please let me die. Let me die. Let me die, please." Before May looked at the wall and saw a big cable, went over to the wall and pulled it out causing the Machine to power down as Skye grabbed Coulson

"Coulson. Coulson. Come back. Come back. Come back. Comeback." Skye whispered as Coulson continued to whimper

"Skye?" Coulson whimpered "Skye…" before he looked up and smiled "Skye."

"Let's get him out of here and back to the Bus." May ordered before she turned to Coulson "Can you walk on your own?" to which he nodded

"I'll grab Raina." Naruto said before picking her up Bridal style


(Several Hours later – Lab – Bus)

Ward, Fitz-Simmons, Skye, Naruto, and May were gathered watching and waiting for Raina to be taken away when May looked at Skye.

"Nice jacket."

"Bet there aren't any flower dresses where she's going." Simmons commented

"Amen to that Baby." Fitz responded before Raina turned to them just as Coulson walked onto the balcony of the second floor where he stood for a moment before walking down the stairs just as Hand started walking up the cargo ramp to meet Coulson

"Just got off the phone with headquarters. Director Fury was very relieved." Hand said

"I understand you've been busy. Heard you put some miles on my plane." Coulson stated

"The manhunt has yielded some impressive results. Centipede operations have been taken down around the globe." Hand explained

"Any word on the Clairvoyant?" Coulson asked

"Nothing yet. But it's going to be awfully hard to stay hidden now that the Clairvoyant's on S.H.I.E.L.D.'s radar." Hand answered

"Good." Coulson stated "Because Raina knew things about me. Personal things. I want to know how."

"My men and I are taking her straight to headquarters for questioning. We'll be in touch." Hand responded before she turned around and started walking away

"Agent Hand." Coulson said causing Hand to turn around "Thank you, for everything." Extending his hand

"Good to have you back." Hand said shaking his hand "Honestly, this bus isn't really my style." Before she turned and walked away

Seeing that they were done talking May, Ward, Fitz, Simmons, Skye, and Naruto walked up to Coulson.

"I just want to say thank you." Coulson said before he turned to Naruto "I want to see you in my office." Only getting a nod from Naruto, they all just smiled for a few seconds "Now get back to work." causing Ward and May to walk away heading for the stairs as Fitz-Simmons headed for their Lab leaving Naruto and Skye, Coulson then turned to Skye

"I heard what you did for me. I think it's time that we remove this." Coulson said before he brought Skye's wrist up to his face "Disengage bracelet." Causing it to beep before it unlocked causing Skye to adopt an 'Are you serious' look

"Are you kidding me?" Skye asked baffled before Coulson took the bracelet off

"I thought you'd like that." Coulson answered

"Back in that room. Did they learn anything?" Skye asked

"No." Coulson answered

"Did you?" Skye asked but got not response "I heard what you were saying."

Coulson simply shook his head "It wasn't real. They were just messing with my head. But I appreciate your concern." Before he turned and walked away heading for his office

"Congratulations on getting the bracelet off." Naruto commented before he walked away heading for Coulson's office


(Coulson's office)

Naruto walked into Coulson's office before he closed and locked the door. Naruto quickly made sure that nothing in the office and no one was listening in on them.

"Am I to assume that you want to talk to me about what I said back at the exchange point, given recent events?" Naruto asked

"I called out to you numerous times. I know you could hear me. But yet you did nothing. Why? And what did you mean by 'Everything happens for a reason, for better or for worse'?" Coulson asked

"When I said 'Everything happens for a reason, for better or for worse' I meant that certain things need to happen to ensure that catastrophic, world possibly even universe-ending things don't happen. There is a main timeline to the multiverse, I am able to see glimpses and major points of that timeline, and I have to abide by those events. I can try my best to minimize the damage from those events, but ultimately they need to happen to make sure that this timeline doesn't collapse in on itself and in turn completely destroy/erase this universe. I had to let you get captured and in turn, tortured, but I knew that you would be alright otherwise I would not have let it happen." Naruto explained "I also expect you to keep this secret, as in level 10 secret."

"Will you keep me informed?" Coulson asked to which Naruto shook his head

"No, because I know for a fact you will try and do something." Naruto answered "Is that all?" Before Coulson nodded his head


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Until next time, Sorcerer12 out, see ya