Section 11 [Marvel/Naruto Crossover]

A lot of my abandoned story ideas are fanfics.  I’m trying to move more into original fiction now, but I have a TON of fanfic ideas that will probably never be finished.  One of my favorites is Section 11.

Section 11 is a Naruto/Marvel/Ghost in the Shell crossover, though the Ghost in the Shell part is mostly context.  “Section 11” is Japan’s version of General Stryker’s mutant force, a team of 11 mutants they send out to resolve situations.  The Marvel heroes (or the X-men, I could never decide who to bring in on this story) only find out about this division when the division’s head, Danzou, sends their tank, “Naruto,” one of Apocalypse’s failed horsemen experiments, to attack the Avengers Mansion/SHIELD/X-mansion. 

I didn’t really have a clear idea of what the plot would be, mostly just of the premise and what the characters would be–Sakura, a failed Dr. Samson clone; Chouji, a Blob-mutant; Neji and Hinata, blind (?) mutant twins who could target internal organs and had a certain telepathy between them; Shikamaru, a robot analyst created by Dr. Shikaku; etc. etc.

I came up with the idea shortly after I’d finished Connecting the Dots, so I didn’t have much incentive to start ANOTHER multi-chapter fic.  I put the idea up as a challenge, and these were the parameters I offered:

Marvel/Naruto Crossover: Section 11

The Marvel heroes (X-men or Avengers) run across the top-secret Japanese military branch Section 11, code-named Konoha. This section can either be a black-ops prison setup, like Colonel Wraith’s facility for mutants, or a simple SHIELD setup where heroes hide out from the judgmental multitude. If you’d rather, you can skip the government idea and make “Konoha” a self-sustaining community hidden underground.

These are no longer ninjas, they’re mutants/heroes. Naruto can still be a demon host (they have those in the Marvel Universe), but the Kyuubi is just a demon. Ino is a straight-up telepath. Neji and Hinata just have weird vision and the ability to target internal organs. Gaara controls sand. No chakra is involved.

Characters: Anyone outside of Lee and Tenten (the normals) can be in this team. (If you really want Lee and Tenten in the story, they should be outside Vigilantes… the Batman and Punisher of Japan.) The leader can be Kakashi, Danzou, or Sarutobi. If you go with the independent community, it can even be Naruto. Anyone from the Marvel Universe can be involved, though because this IS a government thing, SHIELD should probably be involved at some point. Lady Deathstrike, Silver Samurai, Ronin, and Iron Fist are all good characters from Asia who could be used.

Pairings: Anything but Yaoi. I prefer NaruHina but I’m flexible.

Added challenges:

Connect Sarutobi with Aramaki, the leader of Section 9 from the Ghost in the Shell series (they’re twins. I swear).

Sakura is somehow part of the Japanese government’s plan to reproduce the Hulk… or at least Dr. Samson. Her power is related to her hair.

Naruto or Sasuke is involved with Apocalypse.

Neji and Hinata are Twins, not cousins.

Wolverine was at one point part of Section 11. Just because Wolverine has worked for every government and doesn’t remember it at all.

I was really hoping someone else would pick up the idea.  No one ever did.  One person contacted me, saying they wanted to, but they never started or published anything.  I wrote out a few scenes myself, but they hinted at a much larger story than I had interest writing at the time, so I let it go.  But here, now, are the story drabbles.


The brown-haired woman glanced up as the door slammed.  “Ah, Patch.”  She smiled.  “What brings Patch to Japan?”

“Tailin’ a rat.”  Logan picked the cigar out of his mouth and blew some smoke.  “Thought I ought to check in with the local exterminators.”

The woman arched an eyebrow.  “There are many rats in Japan, Patch.  Please to be more specific?”

“This was a young one.  Part of the new crop, I reckon.  Couldn’t be more then… twelve.”  Logan thought for a moment.  “Ten, easily.”

“If boy that young, may not have profile on him yet,” shrugged the woman, moving to the computer.


(As I said, I had a hard time deciding whether this would be an Avengers or X-men crossover.  I think it would probably have been an X-men story eventually, but here’s the same scene from the Avengers storyline.)


“Grasscutter and Green Devil are the local heroes.”  Iron Fist explained as they entered the warehouse.  “Devil actually taught me a lot about hand-to-hand combat when I studied here.”

“Ah-ha, my youthful pupil!”  Devil unleashed a glinting grin and gave Iron Fist a massive thumbs-up.  “Such vigor and enthusiasm!  Had you remained with me, I would have trained you twenty times more.”  He seemed to think.  “No.  I would train you THIRTY times…”

Iron Fist leaned a bit closer to Captain America.  “There are, ah, speculations that Devil is not quite stable.”  He whispered.

Cap nodded.  “Do tell.”

“They’re good folks, though.  Husband and Wife team.  Not sure what their origin is… never really asked.  I get the feeling Lee sorta dragged Tenten into it and she just made sure it didn’t fall apart.”

“Lee is…?”

“Oh, sorry.”  Iron Fist coughed.  “Rock Lee is Green Devil.  Tenten is his wife, GrassCutter.  By day they run a restaurant on the north side.”

“Well, here we are.”  Dropping her guns on the rack, Tenten continued, without even breaking stride, to a large computer dominating the west side of the warehouse.  A few clicks later, the screens flickered into life.  She sat down and pushed her chair forward.  “Now let’s see if we can find your baddie in our databases.  Got any vid files, reports, skin analysis…”  She looked over at the growing silence.  “…anything?”

Feeling distinctly uncomfortable, Captain America rubbed the back of his neck.  “Like we said, he was good.  Put the cameras on a loop, disabled most of the security systems, left no traces.  Apart from the sighting, there’d be no evidence he was ever there.”

“Would you say he was very experienced at infiltration, then?”  Fingers clicked rapidly over the keys.

“No.”  Cap frowned.  “Highly trained, maybe, but not experienced.  His moves were stilted, like he’d learned them from a textbook or a simulation.  And anyway, this was a kid, he couldn’t be more than ten… twelve, at the most.”

The clicking stopped.  Tenten half-turned to look at Cap.  “Twelve?”

“Or ten.”  Cap glanced over at Lee, who had grown curiously somber.  “Is that important?”

Turning back around, Tenten resumed her clicking.  “It might be.  For one thing, we may not have a file on someone that new.  What else can you tell me?  Appearance, abilities…?”

“Blonde hair, blue eyes.  Maybe about 4’9.  Slight build, dressed in an orange jumpsuit.   SHIELD analysts indicate he’s possibly a shapeshifter, though—at least they can’t think of any other way he’d get inside so easily.”

Tenten snorted.  “There are always ways.  What other abilities?”

“He formed some sort of… concussive force from his hands.”  Cap gestured.  “Blew a hole right through the bulkhead.  Freakishly strong.  Also, from what we observed?  He has a healing factor.  Not on Wolverine’s level, but enough to keep him going after a solid hit to the chest.”

“Healing factor…”  Tenten stared at the screen.  “Damn.”  She turned around and glanced meaningfully at her husband.

The two shared a short, silent communication.  Then Tenten sighed, took off her glasses and rubbed her eyes.  “This kid…”  She asked, staring at the floor.  “Did he make copies of himself at any point?”

Cap blinked.  “I hadn’t considered it, but… yes, that would explain his rapid movement through the base and ability to access multiple systems.”

“Did he look like he had whiskers at all?”

“Yes…”  Cap nodded slowly.  “Yes, now that you mention it… he had three long scars on each cheek.  I remember thinking they looked like whiskers.”

“Damn it.”  Tenten sighed.

“I’ll go suit up.”  Lee leapt into the rafters.

Cap glanced from one to the other.  “Then you know who it is?”

Without answering, Tenten reached into her coat and brought out a pack of cigarettes, knocking out a stick and taking it between her teeth.  She remained silent as she lit it, inhaled deeply, and let the ash drift out of her mouth.

Only then did she open her eyes and look at Captain America.  “I don’t know how or why,” she answered, “but somehow you’ve managed to run afoul of the most powerful section of the Japanese National Security Forces.”

Captain America arched an eyebrow.  “National Security?”

“Section 11.”  Tenten clarified.  “Code named: KONOHA.”

“Oh, that’s not the worst of it.”  Tenten shook her head.

“This gets worse?”  Cap gazed at the woman in confusion.

Nodding, Tenten tapped the screen.  “Naruto,” she said, “is one of their most powerful, but also clumsiest, operatives.  Sorta the blunt, heavy object of the department.  Mostly they use him if they need an army taken out.  No way they’d blow him on an infiltration mission, and if they did, there’s no reason he would run from you.”

Captain America slowly nodded.  “They wanted us to see him.”

“Damn right they did.”  Tenten snorted.  “More than that, they probably wanted you to tail him to Japan, though I doubt they figured on you coming to us.  The important thing is, though,  Naruto was meant to draw you guys here.  Which means…”




“Okay, you two.”  The grey-haired commander gestured at the silent pair.  “Hero time.”

With a momentary glance at each other, the twins stood.

The rumble of the airplane’s engine’s nearly drowned out the grey-haired man’s words.  “You’re jumping from pretty high up, but security is tight around here, so wait till the last second to pull the chute.  Once you’re on the roof, sit tight and wait for the signal.  Entry should be through the Quinjet doors.”  His sole eye softened momentarily.  “Most of their team is in Japan right now, so resistance should be light, but this IS the Avengers mansion.  Watch yourselves.”

Two pairs of milk-white, pupilless eyes stared back at him and nodded.

After a moment he nodded back.  “Okay.  Neji, I don’t have to tell you to keep an eye on your sister.  It’s vital she make it to the mainframe.”

“Sir.”  The boy nodded.

“Okay.”  He jerked his head back toward the front of the aircraft.  “Naruto here will be running distraction for you.  He’s going to be breaking into Stark Industries tonight.  That ought to bring whatever Avengers are left here out of the woodwork.”

For a moment, life sparked across the girl’s face.  “Th-thank you, Naruto-kun.”

Her whisper was inaudible amidst the engine’s roar, but Naruto gave a cheeky grin anyway.  “You’re welcome, Hinata-chan.”

“Alright, break it up you two.”  A glimmer of a smile crinkled the man’s eye.  “Now.  Equipment check.”

Quickly the twins patted over their vest fronts, identifying the medic kits, extra rounds, electronic gear, and grenades necessary.  Then they turned to face the door, Neji checking Hinata’s backpack, and the commander looking over Neji’s.

“An UMP 45 isn’t going to do much good, Neji.”  He muttered,  looking over the boy’s weapon.  “These are metas, you might as well be throwing spitballs.”

A smile twitched the boy’s lips.  “A well-placed spitball can make a big difference, sir.”

“Heh.”  The man gave the boy’s back a quick thump.  “Well, you look all set.  Now remember, wait for the signal.  When Naruto hits the Stark Tower, you’ll see it, but unless the Avengers come out, there’s no point to it.  So wait.”

A voice crackled in the radio.  “ETA one minute, commander.”

“Right.”  The man glanced at the twins.  “Helmets.”

Almost together, the two picked up their helmets from the bench and fitted them on, tightening the chin straps.  The rear of the aircraft swung open, exposing the interior to all the noise and fury of the wind.  The commander, now gripping tightly to the roof, gave them a hand-sign, the light turned green, and the two children jogged out the door and leapt into oblivion.

The ramp closed.  Sighing, the man let go of the ceiling and wandered over to sit down across from Naruto.  “Well, that’s done.”  He muttered.  “Nothing more to do about it now.”  His sole eye looked Naruto up and down.  “You understand what you’re getting into, right?  Stark Industries is nearly as secure as SHIELD was, and the Avengers will be on top of you.”

Naruto’s grin was more than a little feral.  “Just so long as I don’t have to run away, like last time.”

“Try not to kill anyone,” sighed the commander, digging a magazine out from under the sheet.  “No point in getting these guys unnaturally pissed off at you.”

“You got it.”  Naruto squinted at the magazine.  “Seriously, Commander, why do you read that crap?  It’s disgusting.”

“You’ll understand when you’re older.”

“You always say that.”

“Commander Kakashi.”  The radio squawked again.  “Preparing for our second run.  ETA to Stark Tower, five minutes.”

Commander Kakashi nodded.  “Right.”


“Director, there’s someone here to see you.”

The man did not turn from the screens.  “Tell them I’m busy.”

“Most unoriginal, Danzou.”  Danzou blinked and turned at the gruff tone to behold a small, wrinkled old man in an immaculate suit.  Sharp eyes gleamed up at him from behind bushy grey eyebrows as the newcomer continued, “I’d expected a more creative excuse from the head of Japan’s black ops division.”

Danzou snorted.  “It is not an excuse.  We have an active simulation in process that requires my full attention.”

“Indeed?”  The other raised a credulous eyebrow.  “May I ask what kind of simulation you are running?”

“You may not.”  Danzou pressed a button on the remote and the screens went dark.  As the ceiling lights flickered into life, he wheeled his way back to the desk.  “I know you too well to hope you will simply leave, so in order to save time, suppose we skip formalities and you tell me what brings the head of Section 9 down here, Hiruzen.”

Hiruzen’s eyes flickered with quiet amusement.  “Aramaki, I think you mean.”

“Oh, is that your name now?”  Danzou raised his eyebrows.  “I keep forgetting.  Tell me, was it really necessary to bring your pet night hawk along?”

Aramaki did not even glance back at the statuesque woman who stood, tall and silent, just behind him.  “The Major is quite capable of discretion and has my utmost confidence.”  He replied smoothly.  “You may console yourself, though… she is here to observe only.”


“Nara?”  The commander’s voice was virtually lost amidst the incessant beeps and whines of computers, the chattering of printers, and the occasional whirr of a cooling fan.  “Nara, you in here?”

“Hmmm?”  A somewhat unshaven, dark-haired scientist looked up from the circuit board he was studying so intently.  “Kakashi!”  He grinned, turning from his work.  “What brings such a famous warrior to the IT department?”

Kakashi’s sole eyebrow hiked upwards.  “You’re a little beyond ‘IT’ here, Nara, and you know it.  As for the reason, there’s nothing special, I just happened to get ahold of some good stuff—“  He pulled a small flask from his coat, “—and thought you might be interested.”

“Really?”  Dr. Nara’s face changed, ever so slightly.  “Well let me just wind up here and we’ll get to working on that.”  Reaching into his coat, he pulled out a PDA and tapped a few keys.  A window on the computer screen opened and closed.

“Okay.”  Face suddenly grave, Dr. Nara put away the handheld and looked up at Kakashi.  “That gives us maybe five minutes.  My handheld will buzz just before the pre-programmed loop ends.  Now what’s this about?”

Kakashi sat down across from Dr. Nara, handing the flask over.  “I was talking to the Chief the other day.”  He said, watching Dr. Nara sip from the bottle.  “And we had an unscheduled visitor of sorts… Aramaki from Section 9.”

Dr. Nara stopped drinking.  “Aramaki?  The monkey man from the cyborg division?  What was he down here for?”

“He was investigating some ‘rumors’ about us breaking into SHIELD.”  Kakashi scratched his head.  “Mentioned there were some American heroes in town causing problems.”

Dr. Nara snorted.  “That’s what Americans do, all right.”  Setting down the bottle, he picked up a cigarette and stuck it in his mouth.  “Well… what about it?  That was a public security mission, Aramaki’s a public security director, just like the chief, we’re not really in his jurisdiction.”

“Don’t give me that.”  Kakashi growled.  “You saw what happened to the Narcotics Team a few years back.  Aramaki’s a public security man, through and through, but he’s a first-rate watchdog too, and if he calls on you ‘unexpectedly’ it means he’s sniffing around.”

“No, I get that, but…”  Dr. Nara plucked the cigarette out and blew smoke.  “….what’s there to sniff around about?  That whole mission was legit.  Not strictly diplomatic, but still, ordinary black-ops stuff, straight from our duly elected authorities.  Frankly I don’t see Aramaki’s problem.”

“Exactly.”  Kakashi nodded.  “THAT’S the problem.  I don’t see it, but I’ve worked with Section 9 on occasion and I’ve heard a lot about Aramaki.  The man has killer instincts.  If he smells a rat, chances are there’s a rat there.”

“And you think… he’s smelling a rat… in our section.”  Nara shifted the cigarette from one side of his mouth to the other.  “A rat so well hidden WE don’t even know about it.”

Kakashi nodded.  “Remember that kid who was here last week?”

“Creepy smile?  Weird locked book?  Yeah, I remember him.  What about it?”

Kakashi leaned further forward.  “That kid had ‘meta’ written all over him.  He should be in our section, but he isn’t.  Danzou knew him, we didn’t.  Danzou commanded him…”

“We didn’t.”  Nara nodded grimly.  “I see.  But… The chief?  A rogue?”

Kakashi rubbed the back of his neck.  “Look, I know I’m not exactly the most unbiased witness when it comes to the chief, but even you have to agree… some of his methods are questionable.  And he’s secretive and paranoid to an extreme.”

“We ARE a black-ops group.”  Dr. Nara pointed out.  “Some would say that’s part of the point.  But… yes.  And given the disagreements you two have had… it’s possible he might organize another independent section to do the missions you’ve refused to lead.”

“Exactly.”  Kakashi nodded.

“Well… what do you want me to do about it?”  Dr. Nara glanced at his handheld.

Kakashi gave a shrug.  “I thought you could maybe poke around the records.  See what turns up.”

A grin spread across Dr. Nara’s face.  “Want me to set my boy on it?”

“Nara…”  Kakashi rolled his eye.  “No, I want you to set that prototype puppet master android you’re constantly obsessing over.  You don’t have a ‘boy.’”

“You’re just jealous of his boyish good looks,” chuckled Nara.


“Oh, my head…”  Bobby groaned.

“He’s up.  That was fast.”  The voice waved, bobbed, it sounded slightly distorted, like a sound in deep water.

“I can put him back under again if you want to.”

“Nah.”  A pair of intense eyes attached to a dark-haired head floated into shape before Bobby.  “Hey, buddy?  You okay?”

“Huh?  Oh yeah.  Yeah, sure…” Bobby sat up, as slowly as he dared.  His skull was still throbbing and his eyes felt curiously hot, but his senses were slowly coming back.  To all appearances, he was in a medical ward of some sort, which was a huge step up from the prison cell he’d been expecting.

“Wait.  So if you’re an empty cyborg body…”  Bobby said, thinking hard, “…couldn’t Dr. Nara have stuck his brain inside you?”

“Yes.  It would have been theoretically possible for Creator Nara to survive his assassination attempt in this manner. I even suggested it to him.”  Shikamaru’s face fell slightly.  “He declined.”


All of a sudden, the square was lit up.  Dark black vans came screeching into the parking lot and surrounded the band.  As the X-men leapt into fighting position, soldiers literally flickered into sight mere feet from them, weapons already raised and pointing.

Through all this, the gene-nins simply sat calmly, watching the scene with an odd air of disinterest.

A small wizened man in an immaculate suit stepped forward into the light, flanked by a beautiful woman and a massive man.  “<Stand down>.”  He ordered the soldiers.  As the men reluctantly lowered their weapons, he addressed the x-men.  “Forgive show of force, Americans.  We had information that there were still hostiles in area.”

Cyclops just looked at him.  “And you are?”

“Chief Aramaki, Public Security Section 9,” responded the old man.  Several of the children looked up at the name.  “Here to take custody of children.”

“You’ve GOT to be joking,” answered Jean.

The woman and man behind Aramaki exchanged a smile.  It wasn’t a particularly nice smile, or a particularly nasty one.  It was more of an aren’t-they-cute sort of smile.

Aramaki just shook his head and reached into his coat to pull out a folded sheet of paper.  “This is document from Home Affairs office, stating that subjects 0-12 are to be given over to me, as well as Dr. Nara’s puppet droid.”  He handed it over to Cyclops, who took it wordlessly.  “Chief Danzou has been removed from his position, and Section 11 has temporarily been frozen, pending internal investigation.  Until new director appointed and new facilities created, meta-humans have been placed under guardianship of Section 9.”

“Short answer: No, he’s not,” grunted the big man.

“We appreciate American assistance in this matter,” continued Aramaki.  “However, we cannot allow such powerful resources to leave our country.”

“These aren’t just resources, damnit, these are CHILDREN!”  Cyclops shouted.  “We can’t just allow you to take them back to new underground prison you’ve made up for them!”

The old man’s gaze did not waver.  “Permission is not needed.  These children are wards of state.  X-men have no jurisdiction over them.  If X-men attempt to kidnap them, X-men risk causing international incident.”

“You honestly think we care about that?”

The old man closed his eyes for a moment.  “American disregard for state affairs is well-known.”  He answered.  “Particularly that of X-men.  However, thousands of lives are at stake here.  Taking children out of country similar to removing half of country’s nuclear arsenal.”

“Half?”  Jean raised an eyebrow.

Again the big man smiled.

“Such course of action would be undesirable for both countries.”  Aramaki observed.  “Japan would not appreciate such disarmament, and America would be uneasy accepting 11 new walking bombs.”

“They might feel better about accepting 11 fugitives from the Japanese government.  Fugitives that you caged up and used as child soldiers for your own purposes.”  Cyclops snorted.

“With all due respect, it is doubtful America wishes for people to be reminded of such things,” commented Aramaki drily.  “Unpleasant memories might be aroused.”

Cyclops turned to Wolverine, who had been standing off to the side, smoking in silence.  “Feel free to jump in here any time, Logan.”

Wolverine shook his head.  “Sorry, Summers.  He’s right.”

“Logan, don’t tell me you’re going along with this.” Jean threw him a look.  “We can’t let them just lock these kids up again!”

Aramaki sighed.  “Major.”

The woman stepped forward, closer to the circle.  Cyclops held up a warning hand, but she kept on walking, as if unconcerned.  Stopping in front of Naruto, she kneeled down to his level.

“Naruto, right?  Subject 0?”

Naruto just nodded wordlessly.

The woman smiled.  “I’m Major Kusanagi.”

At the word ‘Major,’ Naruto looked up.  “I killed Chief Danzou.”  He said, his voice curiously quiet.

“Yes, I know.”  The Major nodded.  “That was sloppy.”

“I didn’t mean to.”  Naruto looked away.

“It’s not a serious problem.” The woman assured him.  “He would have been executed anyway.  But we would have preferred to question him.”

Naruto still looked down.  “Sorry.”

“Do you understand what’s going on here, Naruto?” asked the woman.

Looking up, Naruto shook his head.

“Naruto, these people want to take you away,” said Major Kusanagi.  “They want to take you away to a new place, with new people and a new language.”

“Look here…” Cyclops began, but Jean silenced him with a wave of her hand.

“It’s a good place.  You’ll probably have better housing conditions than you have here, and you’ll meet more people.  They’ll train you how to keep your powers under control.  And you’ll never have to go out on missions if you don’t want to.  You’ll be free to do whatever you like.”

“Really?” asked Naruto.  He looked curiously troubled.

“Yes, really.”  The woman nodded.  “But…”  She leaned in closer, “You’ll be exposed.  People will know about you.  They’ll call you ‘unnatural,’ and ‘demon.’    The people will constantly be defaming you, attacking you, even, and your friends with you.”

With a start, Bobby realized that all the gene-nins were silent, listening to the woman.  She wasn’t just talking to Naruto.

“Technically your new friends will protect you,” continued Major Kusanagi. “And you won’t have to leave the refuge if you really don’t want to.  But you’ll be expected to try to fit in among the humans—like them, protect them, even.  They’ll expect you to protect the people who hate you.  And you will NEVER be allowed to kill.”

Naruto’s troubled look grew.

“You’ll never go out on your old sort of mission, Naruto.  You’ll never kill, and if you ever DO kill, even by accident, they will never let you forget it.”

“I killed Danzou.”  Naruto repeated.

“Yes,” nodded the woman.  “And they were shocked by that, weren’t they?”

“I… I didn’t know what I was supposed to do…”

The woman smiled.  “They won’t tell you.  They’ll never tell you what to do.  There’ll be no schedules, no protocols, no orders.  There’ll still be training, and missions, but what you do with that knowledge will be up to you.  It will be your responsibility.”

The idea was to fit the ending within Ghost in the Shell’s more cynical view of the world, where politics trumps justice.  But it would end with the new Section 11 being headed by Chief Tsunade, a genetics scientist distantly connected to Aramaki, and the overall intent was that even though the kids were still working for the government, their situation had noticeably improved.

I think there’s a lot of potential in the idea, but it’s a lot more work than I want to get into anymore.  Though still, open to any takers!

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