The Root of Darkness Chapter 2: Root Training, a Naruto + Harry Potter Crossover fanfic

Disclaimer: I don't own Naruto which makes me sad.

I looked towards my instructor and even though I know she is female it's hard to see it through the probably intentionally baggy clothing and blank mask that hides her hair and face. She motions me to follow and I climbed out of the bed to do so. Still without talking she led me to one of the walls and upon nearing it a section sinks into the ground allowing us out of the room into a dark grey corridor similar to the room. A noise behind me catches my attention and I watch as the section of the wall rises back up and seals off the room. Some kind of Earth manipulation probably.

My new sensei leads me through the purposely similar maze like corridors until we stop at another blank section of wall which like before sinks down to admit us to some type of lab. Another androgynous person in a mask is waiting for us, at least this one speaks.

"Sit on the stool here." The doctor commanded. I did so and he started attaching monitors to me. "Before we start training you we need to know what level you are already at and if your bloodline grants you additional features that aren't readily apparent. To do that we will need to do some testing first. Some of these tests will be painful or stressful but you will need to move past that. Do you understand?" I nod and the battery of tests begin.

It seems pretty normal tests for strength, dexterity, reflexes, memory retention stuff that seemed to be standard tests. Then we got to test my healing factor. The doctor made a little cut on my arm that completely healed within a minute. What I assumed raised eyebrows was how it healed. One minute it was still bleeding and the next it was fixed. No visible healing just blink and you would miss it. The doctor took it well and made a series of small cuts with one longer one on both arms that healed one by one in the same fashion as the first. The longer one healed in parts but still the same fashion as the others.

The doctor made some notes and thankfully moved on to the next test. This one involved Chakra and how fast I regenerated it. The doctor attached another node to me and told me to expel a quarter of my Charka. I did so and we waited for about an hour for it to fully recharge. It was probably foolish of me but in order to receive better training I explained that I could regenerate Chakra if I fell into a meditative state. He had me do the same exercise again except this time it took 2 minutes for me to fully recharge. A momentary pause was all the reaction I got before the doctor finished writing on his clipboard and dismissed both of us.

My sensei led me through even more uniform tunnels to what seemed to be a storehouse for equipment. My sensei blurred away and returned with a bundle of clothes which she gave to me to put on. The chainmail mesh went on first then the darker clothes on top with open toed sandals for footwear. Finally the full head facemask went on last covering my white hair and adhering to my face. I knew that they had to see out of the mask somehow but it still surprised me when, after a brief moment of blindness, the mask turned transparent to my view and I looked around marveling at it. Getting over it soon enough I finished putting two kunai pouches, one on each leg, and five shurikens up each sleeve. I had to get help with the last part.

That over my sensei led me to a large open room with posts with numerous nicks and gouges on them. Going to the center of the room she turned to me and spoke for the first time. "Impress me." Then there were kunai flying at me. For the first time I could actually sense her Chakra and knew that she was doing it for my benefit. I barely had time to process the fact before I had to dodge, one kunai slicing a line through my arm when I didn't dodge quite fast enough.

Quickly palming a kunai and chucking it at her, and ignoring the resulting pop up, I blurred through the hand signs creating a clone that went right while I went left. She dodged it of course. It was almost lazy the way she did it, moving not an inch more than necessary to dodge. That was fine it wasn't meant to hit her. With a twitch of my finger the Chakra string attached to it sent it flying at her undefended back. Once more she dodged with enviable grace not that I expected anything less.

Making the clone stop and look like it was controlling the now attacking kunai I sent my Chakra inward, empowering myself and ignoring another pop up. Palming another kunai I charged forward towards my sensei where she was now lazily slapping away the kunai when it got too close. I charged faster and faster until I was right next to her arm poised to strike when it felt like a mountain crashed down on my face sending me tumbling away.

I didn't land very well rolling along the ground as my fingers lost their grip on the kunai sending it flying away. I stumbled to my feet, cheek aching, to see her arm still extended and palm out. She bitch slapped me an incredulous portion of my mind spoke up before she was right in front of me and oh there is her leg. I must admit I have no idea how to move my body in a physical fight so what happened next was a complete and utter slaughter at close range fighting. When she seemingly tired of using me as a human punching bag she held up her hand in a stop motion and spoke for the second time. "Pathetic."

A mixture of shame and anger welled up within me before being smothered by calm. "I know sensei." I stood with some difficulty and eyed my stats, half health and a quarter Chakra left, enough for now.

"Good. 200 pushups, 200 situps and 50 laps around the room. No Chakra. Go." A woman of few words. I pushed my aching body into the exercise while looking at the pop ups I dismissed earlier.

Ding!

Learned Chakra Enhancement (Active 15/min) LVL 1 – 63%

Chakra can be used to enhance the physical aspects of your body leading to an increased performance. Careful not to push too hard or you might break something.

Increases STR, DEX and END by 5%

Ding!

Learned Kunai Handling (Passive) LVL 1 – 15%

You can use a kunai without stabbing yourself… probably.

10% increase in accuracy

Ding!

Learned Pain Tolerance (Passive) LVL 2 – 3%

Where others falter you can continue.

2% chance of ignoring pain when dealt an injury.

A pretty good haul of skills for being beaten up. It's a far better use of my time than trying, and failing, to improve myself at the orphanage without anyone noticing. So what if I'm recruited into a secret organization in the shinobi world. I never expected the world to conform to the show where Naruto can use his therapy jutsu to make everything better. No, this is a world of death and I need to grow strong enough to survive it. If that means my ledger becomes red with the blood of others so be it.

Ding! For realizing the necessity of a plan to survive take +1 WIS, +1 INT.

I could feel my sensei's gaze snap to me at my sudden surge of Chakra. 'Oh, so that's how they found me.'

Ding! For realizing how Danzo's people found you take +1 INT. 'Shut up.'

~Interlude~ Danzo

An interesting report came in from one of my non-field operatives manning an orphanage to search for talent that could be used for the betterment of Konohagakure. A one year old actively using Chakra. That's abnormal even for ninjas. A quick order for an increased watch over him and he turned his attention back to reports from the front. After all he had a war to win.

Even with events on the border becoming increasingly bloody I was intrigued enough by the reports about Shiro to attend to him myself as he was brought in. The order was sent and he was quickly processed and brought to one of my bases in Konoha. He didn't look like much but then appearances are always deceiving and even with the emerald eyes and white hair he still looks like a normal child.

I had to snort at that 'normal' nothing he does is normal or he wouldn't be here. Oh well time to get this show rolling. Everyone has their Chakra suppressed to keep him off guard if the reports of him being a Senor are true. He's awake now and not seeming to panic in the slightest at his predicament, good. He begins probing me for answers, not subtle in the least but that can be excused by his age, and I give him non answers. Finally I give him a chance to brag about his bloodline, maybe show off a bit and make him reveal something he hasn't already shown us.

Asking for an E-rank jutsu scroll was odd but doable. As he picked up the scroll Saiko settled in behind him garrote held around his neck. When the scroll started dissolving into light I had to quickly order her not to kill him. Then the brat goes and uses the Clone technique written on the scroll saying he 'ate' the knowledge that it held. Sadly it doesn't work for a report on population census in a neighboring civilian village but the potential for this is still extreme. It reminds me of the Uchiha's eyes almost but without the potential genjutsu usage. Probably for the best. I also saw the tiniest flicker of annoyance as the scrolls keep on appearing and disappearing without his notice. The others in the room were also amused by it.

I decide that he has too much potential to waste going the conventional route through the Academy and give him one final test by seeing how he reacts to my philosophy. His answer… surprised me. It brought out long held memories of fighting and the dying screams of my enemies. It actually brought a smile to my face. One that I noticed Saiko shivered at while he stared at me intently. He'll go far or burn out, either one. I left him to Saiko and left the interesting diversion from the war and paperwork behind. Damn paperwork.

Saiko flickered into being before my desk head bowed and on one knee. "Report." She brought out the medical report going over the impressive healing factor and astounding Chakra regeneration in detail before going over his training test.

"He has a good tactical sense using a combination of diversions and misdirection to achieve his goal. He also seemed to create and use a technique, Chakra enhancement, on the spot with no prior training. In an attempt to goad him into an emotional response he remained calm throughout. He doesn't seem to have any training with taijutsu. In addition he had two more spikes of Chakra gain right after the fight. Right now I have him exercising."

Hm, sort of like pushing himself to the next level when faced with adversary. I considered the report before dismissing her. The Shadow clone popped and I was left with my mountain of paperwork. I eyed it distastefully and decided to bring my new member to Hiruzen's attention. After all the Root supports the tree.

~Interlude End~

I came to a rest as I finished my laps. Breathing deeply I faced my sensei and received the barest nod of approval. She tossed me a scroll and commanded me to eat it.

Ding!

Learned Beginner's Leaf Taijutsu (Passive) LVL 1 – 20%

Basic katas at the beginning level of martial arts. It won't impress anyone but at least you know it.

Increases DEX and STR by 10% while using.

"Do you know it?" I nod. "Good go through the katas." I go through all 20 of them with her calling out flaws and correcting them. I finished the set and she orders me to do another set of the same exercise as before. This goes on and on for what seems like hours although it's hard to tell without the sun until finally she stops me.

As meal appears before me and I shovel down the bland tasting meal with gusto. I'm a growing boy after all. I didn't even see her bring the meal but that's not saying much. As soon as I'm done my plate disappears and in its place a mound of scrolls almost as high as I am appears. I look back and forth from my sensei to the mound of scrolls. "You don't need sleep yes?" I feel like I shouldn't but I cautiously nod. "Good. See if you can eat any of these." I shift through the pile but no pop ups occur and I inform her that I can't. "Alright, read these, don't leave the room. Bathrooms over there,' a section of the wall sinks to the floor, 'if you need anything say it out loud. I'll be back after I wake up."

With that she vanishes leaving me 'alone' with the mound of about 50 scrolls or so. I stoically pick up the first one and begin reading. At first I miss a few words but as time goes on I miss less and less until my reading comprehension reaches 100%. I've gone through 20 scrolls by now and I decide on a quick break to test out the new techniques I have.

Chakra flows through me as I test throwing my kunai at the targets with and without enhancements. Testing the difference in strength and speed. I draw the kunai back with Chakra strings until I have to meditate to recharge. Sitting down I meditate until I'm topped off when my stomach lets out a hungry growl. The sound confuses me for a moment. I don't get hungry anymore so why would my stomach growl? I shrug mentally and almost sheepishly ask, "Can I have some food please?"

Another bland meal appears before me. I'm getting kind of annoyed at that actually. Yes, I know you're impossibly strong compared to me you don't have to keep rubbing it in my face. Finishing off my meal I return to my studies managing to finish everything right before my sensei shows up. I guess that's the end of day one.

Ding! Gained +1 LVL Chakra Enhancement, +2 LVL Kunai handling, +1 LVL Chakra manipulation +6 INT, +3 WIS, +3END, +1 VIT, +4 STR, +2 DEX

Name: Shiro

Age: 2 year - 0 months

Title: Root Shinobi in Training

LVL: 5 - 5% to next LVL

HP: 170/170

Chakra: 1085/1085

STR: 16

VIT: 17

END: 21

DEX: 16

INT: 18(18.36)

WIS: 15(15.3)

LCK: 11

Points: 25

Money: 300

My sensei just stares and stares at me in silence the next day after she appeared. I don't say anything and neither does she for the longest time. I start to fidget after a while. "Brat, what kind of monster are you?"

"Excuse me?" She continues on as if I didn't talk.

"When people think of a prodigy or a genius they think of someone who can master anything effortlessly. You on the other hand seem to fit in the same category yet in just one night I can feel how much more potent your Chakra pool is. Your bloodline makes you a giant amongst those we call geniuses and that's why you're a monster. That's fine though, as long as you're our monster and can use that power to protect the village you will always be accepted. You may be feared but accepted all the same. On the other hand,' I can feel her glare sharpen on me even through the mask,' if you abandon the village you will be a monster to everyone and no one will protect or accept you. Do you understand?"

I can't let that pass without comment it would be bad. Slowly my hand reaches up and removes the mask. My normally calm face set into a scowl. "Sensei you get a pass this time, but question my loyalty again and I'll train and train and train until I'm strong enough to beat you black and blue." Having said my piece I slide my mask back over my face. "Now what do you have for me today?" A silence falls between us before she starts barking out commands. I feel as though I've passed some silent test and for that I'm grateful.

Days turn into weeks, into months and I finally learn my sensei's name, Saiko, along with asking a question that's been bugging me since I got here. "Saiko sensei, why can't I Sense anyone's Chakra here?" She finishes her throw and the shuriken flies towards me which I deflect with a clang. I kept running through the obstacle course as she takes her time to respond. "We suppressed our Chakra's natural leakage from our bodies once we knew you were coming."

"Tch." Finishing a particularly difficult contortion in midair to avoid being impaled I continued talking. "So you knew I was a Sensor."

"Nope." I nearly faltered at her downright cheerful tone but managed to slide/duck under the next blade. "Thanks for confirming it though." This time I did stop before her barrage of weapons forced me to jump over the spike filled pit.

"I messed up by giving away information, didn't I?"

"Sort of. You did well at keeping your ability a secret for so long but in the end we had our suspicions and you merely confirmed them. Just remember the shinobi world lives and dies on information. Guard it well and seek it like it the most precious gold yet don't keep information from Lord Danzo or Lord Hokage. They need to know for the betterment of the village. Now since our little monster has revealed yet another talent let's stop this for now and I'll set you on the Sensor course."

I stop running through the death- I mean training course and follow Saiko out the door. The corridors are still as confusing as ever yet she unerringly leads me through the twists and turns until we arrive at a door with only darkness beyond. "This,' she motions towards the darkness, 'is a sensory deprivation room that will only allow you navigate by sensing the Chakra in the room. To that end,' she stabs me with a needle, 'we use this drug to take away the sense of touch."

I ignore the ding as she wraps a cloth over my mask, not really sure I need it in a pitch black room but okay. "Before I block your hearing can you still feel?" I nod and with a put upon sigh she stabs another needle into me. Now I can feel it or rather I can't feel anything at all. "How about now?"

"I can't feel anything." She does something to my ears and all sound vanishes. A force on my back sends me tumbling into the room and I think I hit the floor or something. All I know is that I can taste blood. It's almost eerie how similar this place is to the void after death. I would panic but Gamer's mind saves me again and all I feel is calm as my Chakra sense stretches out.

I can feel it after an unknown amount of time. Like a trail of breadcrumbs it leads to a shining beacon in the darkness. Trying to stand fails so I am left to crawl my way towards the beacon. I can feel it getting closer and closer and once I am close enough to reach out and touch it the beacon vanishes. I'm left in darkness once more until I sense a fainter beacon in the distance. Once more I resume my crawl. The cycle repeats over and over until there is nothing left and I can feel myself being lifted up. Everything is returned and now everything is too bright, too loud and too clear. I nearly pass out but I hang on long enough for the deluge of information to clear.

Ding! For extreme training gain +10 LVLs Chakra Sense

Saiko lets me rest for the rest of the day which is an unusual treat. I spend it meditating and coming to terms with having all my senses back. The next day is back to the grind like nothing ever happened and time continues to pass by.

Several more months pass before Saiko sensei moves on to the genjutsu portion of my training or rather the identification and nullification of hostile genjutsu upon my person. I have mixed feelings about the subject. On one hand I dislike the idea of messing with another person's perception of reality and on the other hand I don't know if genjutsu will even affect me.

The time comes all too fast and Saiko finishes a set of hand seals that does nothing. Nothing changes and a quick check of my body and a glance around reveals nothing out of place. "Sensei what was the technique supposed to do?"

"You don't see anything?" I shake my head. "It was supposed to show you your darkest fear. Hang on this one will make you feel like bugs are crawling in your skin." That sounds unpleasant.

The hand seals finish and once more nothing happens. I feel the need to sheepishly rub my head before it gives way to calm. "Sorry sensei nothing."

"Wait here." Wow she sounded kind of annoyed. A few minutes later Saiko returns with another Root Shinobi. "Tap the side of your mask and look into his eyes." A portion of my mask slides away revealing my eyes. Emerald met red and nothing happened. A lot of that is happening today. I look back at my sensei and shake my head in the negative. Commanding me to resume my exercises they both disappear.

~1 Year after joining Root~

Saiko sensei leads me through the maze like tunnels which still confuse me even after a year here to a room where Lord Danzo is waiting. I kneel, as does Saiko, and I await him to acknowledge me. A twitch of his finger and Saiko melts back into the shadows, dismissed. "Saiko has informed me that she feels you are ready to take your final test to become a Root Shinobi."

Ding! Quest Alert Shinobi of the Root

Lord Danzo has one final test before you can stand and fight with the proud Shinobi of the Root for the protection of Konohagakure. Follow him and complete your test.

Rewards: 3000xp, 500ryo, title Root Shinobi

"Yes, Lord Danzo, I am honored sensei considers me ready and I will not disappoint her in this." A noncommittal hum as he motions me to follow him through the doorway. I smoothly rise and follow three steps behind him to his left as is proper. The room has nothing but a young woman strapped to the wall. Various wounds littler her body and only the bare amount of clothes protect her modesty. For all her horrific wounds her eyes still dart around the room and from time to time I can see her testing her bonds. I take in all of this before Lord Danzo speaks again.

"During missions for the village you will be called upon to take another person's life. Whether in battle or when they lay helpless before you. To know that you will not hesitate we test you so that your hesitation will not get other shinobi killed. Remove your mask, take this kunai and kill her. Remember a shinobi's duty is to complete the mission, without remorse, without feelings."

Slowly my mask is removed and I take the kunai from his hand, careful not to scratch him, and walk towards the chained woman. She heard what Lord Danzo said and her attempts at escape are far more frantic now, eyes darting everywhere. I draw closer and closer while realization dawns in her eyes. My arm moves, hundreds of hours of practice set into motion, one strike through the fleshy part of her lower jaw and into her brain. She gives one last, wet, desperate gurgle then falls still. Her body slumping against her bonds.

"Congratulations Shiro you are a shinobi of the Root now after killing an Iwa chunin." I feel a hand on my shoulder and look back to see the unmasked face of Saiko standing behind me with a slight smile on her face. I should feel horrified at what I've done, shocked, angry, sad yet all I feel is calm and at that moment I realize Saiko is right I am a monster.

Ding! Quest complete. Gained Level up X 3, title Rookie Root Shinobi, 500ryo

Rookie Root Shinobi: When equipped gain a 20% increase in stealth

Name: Shiro

Age: 3 year - 0 months

Title: Rookie Root Shinobi

LVL: 8 - 1% to next LVL

HP: 590/590

Chakra: 8,550/8,550

STR: 61(67.1)

VIT: 59

END: 63

DEX: 75

INT: 53(54.59)

WIS: 52(53.56)

LCK: 13

Points: 40

Money: 800

Skills:

Chakra Control

*Chakra Manipulation (Passive) LVL 60 – 0%: Chakra is what you and others will live and die by. By controlling it you stand above others.

Decreases the cost of active techniques by 15%

Increases Chakra control by 60%

Increases Chakra Capacity by 30%

Tree Walking (Active 30(25.5)/min) LVL 10 MAX

An exercise meant to promote Chakra control and grow reserves.

Increases Chakra Capacity by 25%

Water Walking (Active 40(36)/min) LVL 10 MAX

An exercise meant to promote Chakra control and grow reserves.

Increases Chakra Capacity by 25%

Ninjutsu

*Clone Technique (E-rank) learned (Active 50(42.5)) LVL 10 – MAX

The Clone Technique creates an illusionary copy of the creator that can move around at the creators command. This is one of the three techniques necessary for any aspiring genin. Warning clones do not have shadows.