AN:
First of all, I apologize once again for abandoning this story. It fills me with enormous guilt, I assure you, but the original spark just isn't there.
Second, I have to apologize again, this time for how long it took me to upload an outline of the story. Though, in my defense, I did say that I only might do so.
Third, if anyone still has questions after the following explanations and summaries, then feel free to review the story or PM me. I will try to answer questions, and if they hit a relevant point that I neglected to mention, then I will edit them into the context of this chapter. All edits will be dated so that people don't have to read the whole thing again to find the new stuff, if they feel so inclined.
Fourth, please thank Brian B for this outline: without his questions I wouldn't have found the inspiration to type it all up, and my large pile of post-its would still exist.
And lastly, I do not pretend that this is a work of art: the tense changes quite a few times, there are grammar mistakes galore, and perhaps a bit more sarcastic humor than I meant to include. I at least tried to order things into a table of contents to make them easier to find. Also, I am no professional. This is all sci-fi-ish at best.
Thank you for your interest in the story, and happy readings!
-Itallia
Humane Studies Notes
Contents in Brief:
A. Basic Story Plot
1. Shino's Dilemma
2. The Game
3. DNA Testing
4. The Scanner
5. Therapy
6. Portal
7. The End
B. Chakra Explanations
1. Basic Chakra
2. Specific Examples
3. Spiritual and Physical
4. Bloodlines
5. Kyuubi and Kimimaru
C. Shinobi Profiles
Subject A1: Rock Lee
Subject A2: Hatake Kakashi
Subject A3: Aburame Shino
Subject A4: Tenten
Subject A5: Nara Shikamaru
Subject A6: Hyuuga Neji
Subject A7: Uzumaki Naruto
Subject A8: Yamanaka Ino
Subject A9: Uchiha Sasuke
Subject A10: Inuzuka Kiba
Subject A11: Hyuuga Hinata
Subject A12: Akimichi Chouji
Subject A13: Haruno Sakura
A. Basic Story Plot
I had planned for several key events to happen while the shinobi were under the scientists' tender mercy.
1. Shino's Dilemma
The next chapter was supposed to be the start of Shino's rapid and alarming health decline. The "uncomfortable warmth" he felt in Interviews was fever. But Shino has never been sick before: his bugs protect him from all manner of germs and bacterium. Without them, his immune system is intensely weak—he'll basically catch anything, and then be very slow and inexperienced in fighting it. So the scientists freak out about this for a while. Eventually they realize what's happening when the bugs start dying as well (no food, they need chakra). Shia releases the bugs into Shino's room, hoping to set things to rights.
Shino gets better and his bugs feast, and then as soon as someone else opens the door, they pour out on Shino's command and flood the center. Since the scientists have no chakra, the bugs can't really do anything to them (except freak out a few personnel; the screams will ring), this throws things into chaos. Shia performs a scan for chakra sources in the building, and in that way pinpoints most of the bugs. A few clever ones hide near larger sources of chakra—a few of the other shinobi, the Atom Splitter device, etc. The Tech team devises a way to contain Shino and his bugs together in a way that would allow the scientists to visit him still. It involves a little room that separates Shino's SR from the main hall, and threats to his bugs' welfare. He, naturally, complies with the whole thing, and gets a few spies out in the main area as a bonus.
2. The Game
After everyone got settled in and the scientists were done exclaiming about the various unique qualities of their subjects, I had planned for Raifu, Head of Technology, to excitedly finish his "pet project." This would be a device that simulates environment, much like a virtual reality game. The scientists would then put the shinobi into this "game" in an attempt to learn more about their abilities.
The game works by interpreting neuronal messages in the brain and changing circumstances according to the players expectations. This means that if you are walking down the street expecting a dog to attack you, it will happen (unlike in real life, where you may be wrong). For the shinobi, this means that if they expect their shuriken to cut through steel, it will do so. Every good shinobi knows his or her own abilities, so nothing happens without the shinobi expecting it in this game. Except (of course there's an exception) for the basic override system that Raifu installed. With this, he can control (to some extent) the NPCs (for non-gamers, this is Non Player Characters), which in this case means the scientists. The setting Raifu creates is exactly how the shinobi are in real life—in their individual rooms, bolted down. They place the gear on while the shinobi are asleep, so when our beloved ninjas wake up and begin their various escape plans, expecting them to work, they do work. Except, of course, that it's only in the game. I had planned to do all this in a way that you, the reader, would not realize that it's all fake unless you correctly interpreted the scientists' cryptic remarks about the game and the various little hints you'd receive from the shinobi POVs, or until we finally switch from the shinobi POVs back to the scientists, who had been watching their rampage in horrified fascination on television screens.
The escape and attack rule is especially true for Kakashi, who finally comes out of his mild coma while under the game's influence. He is a bit enraged that the chakra for his genjutsu mask ran out while he was asleep, his sharingan eyeball hurts, and it's the first time he's ever been captured by enemies. He's pissed (Kakashi style), and not just at his captors: he's also upset with the younger ninja, most notably Shikamaru, since he put the guy in charge and he's the only chunin among them. So he escapes, casually slaughtering various scientist personnel on the way, and begins the arduous task of rescuing everyone.
Eventually, the scientists tire of seeing themselves be killed and turn off the game. Cue ninja rage at finding out that a "very powerful genjutsu" had gotten their hopes for escape up. Thankfully, it was not all for naught: the scientists now understand not only some of the shinobi abilities better (or at least how they interpret their own abilities and each others'), but they understand what exactly the shinobi will do if they escape. Tensions between scientist and subject or, not surprisingly, high. An interesting exception to the general "kill/knock out/maim and run" rule is Shino, who has been watching the scientists through his bugs and is slowly realizing that they're not truly "evil"—they're not even out to harm the ninjas. So while he's not exactly sociable with them, he's more inclined to merely run away from them instead of attacking.
This game would be employed at least the once, perhaps more.
3. DNA Testing
After the first virtual reality experience, the genome testing results would come in. Insert scientists' geeky squees. For more information, see Shinobi Profiles.
4. The Scanner
The chakra scanner that Raifu was making will be completed and with it the scientists will be able to pinpoint specific chakra hot-spots on the bodies of the shinobi. Some examples would be Sasuke, Neji, and Hinata's eyes, Naruto's seal, and Ino's brain.
5. Therapy
Kire, Head of Psychology, would set up a schedule for "therapy" sessions with the ninjas who need it. Many things would be addressed during this, such as relationships between the shinobi and their pasts and home lives. For more information, see Shinobi Profiles. To do these sessions safely (for the scientists), they use a variation on the virtual reality game. The therapist and ninja enter a private world with the gear and can talk that way without physical threat to either of them. Several of the therapists and ninjas would become close in these discussions, or at least learn a bit about each other. The therapy sessions were to be a very big part of the story, and the place where the most character development happens. For more information, see Shinobi Profiles, subsection "Psychology."
6. Portal
The scientists would eventually understand Kakashi's Sharingan enough to duplicate his portal-opening abilities. After some technicalities (tracing electronegative signals and whatnot), they would eventually create a machine that opens a portal back to the Naruto universe. This is important for the next part, The End. Read on, please.
7. The End
The end of the story is rather complicated. The beginning of the end starts with Mr. Dover, the boss of bosses, telling Shia that they are transferring this experiment to another group and that she and her team will be sent back to Japan. Reason stated for this change: he has monitored their progress and decided that some of them have become too attached for their own good. The monitoring would have been done by a spy in their ranks, one of the "helpers" who is bitter about her lower place in the hierarchy.
Of course, it's entirely true: Shia and the rest of the scientists will have become rather attached to their strange subjects. And so Shia would argue with herself for a while, have a short moral and philosophical dilemma, and then make a decision and plan carefully with Shikamaru and the other shinobi. The shinobi would be doubtful at first, but after prompting from Shino, who's been learning of their essentially good intentions, and Shia's manipulations ("Would you rather stay here forever?"), they agree to the plan. When the new team arrives to take over, she would stage an elaborate scene that allows the shinobi to escape, using the portal to go back to their world, and then make it look like it was all her idea and the others involved were merely following her express orders, as they are supposed to do. Mr. Dover would arrive in person as she explains this and she would be particularly smug in forcing his hand, because she would have done all this in such a way that it becomes difficult to simply kill or arrest them all without looking like a tyrant. After all, this is America, home of justice and all that good stuff, and Mr. Dover has to keep up appearances in front of the new team who came to replace them, or bad word would get out and he would be demoted or worse. After all, he still has a boss to answer to: the American government that pays him.
And so everything would go as the scientists planned (of course the others were in on it!): Shia alone would go to jail, the shinobi would be sent home without a way to trace them back, and the rest of the team would merely get laid off/fired for incompetency or whatever excuse Mr. Dover comes up with. There would be a short scene to wrap up the fate of the scientists: Shia in a prison cell at the point of time when several of the other scientists break in and help her escape. She'd make some comment about it taking long enough, ask where they're going now; someone would suggest Fiji, someone else would suggest rebuilding the portal machine and finding a completely new world, etc. The scientists would leave the gaping inmates chatting in this strain.
Back in the Naruto universe, everyone would of course report to Tsunade and explain what happened. (No time will have passed since their leaving, which means that there are enraged Akatsuki members out in the forest somewhere.) Then they'd all start their various "make myself better" campaigns, and things would go back to normal. For more information, see Shinobi Profiles.
And that would be the ending!
B. Chakra Explanations
1. Basic Chakra
As already explained in the story, chakra is the energy that results from radioactive decay after the splitting of an atom. The specific atoms that are split are particles of condensed ATP energy, otherwise known as heavy particles. These are split and the resulting decay energy is stored as chakra. The bodies of people from the Naruto universe are born with the ability to do this split and then break down the energy. The chakra can then be used for virtually any purpose as long as the proper manipulations are made to it. As science will tell us, matter can be made by smashing enough energy together—this would be how you would create physical things from matter, like Naruto's Kage Bunshins or something as simple as water. Energy can also alter forms, so fire and lightning, etc, are also possible. The Naruto hand signs are rather like directions for the energy in the same way that moving a certain muscle in your arm is necessary to move a muscle in your finger.
I had planned for there to be a special, unique compartment in the brains of the Naruto characters that is the mental center of chakra control. Chakra, to them, probably feels something like a fifth limb or a sixth sense—though, like any muscle, it has to be exercised to function properly. I had also planned for there to be a critical period to learning chakra control—if it's not started within a certain age range (the ninja academy age), then the ability to control and increase chakra potential will be lost. (Fun Fact: Humans have a critical period for learning how to speak that's somewhere around age 2.)
The splitting of an atom and subsequent energy processing would happen in each cell. As we know, splitting an atom causes a massive release of energy—the whole ability of chakra creation lies in not creating an explosion, and instead taking that energy and filtering it down to chakra. Shinobi actually get very little chakra, comparatively, from each atom split. Each cell stores the chakra it makes, but there is naturally a limit per cell. This limit can be stretched and increased with practice, which then increases chakra potential. If the limit is exceeded, the excess chakra will leak out. Without this ability to leak, the extra particles will lyse the cell.
2. Specific Examples
As described in section 1, this cell lysing is what happens with Chouji and his clan when they use pills to artificially enhance their chakra output. The pills increase chakra control to the point that it prevents the chakra from leaving the cells without a mental command, and so the cell lyses. Normally, the chakra would leak out on its own when there was too much build-up (like what happens to Naruto when he releases chakra uncontrollably—it's because he's making too much to hold it all with his current capacity, and he doesn't have enough control to keep it in.) So, by taking the belt off of Chouji, Shia released the chakra that had, without an outlet, been building in his body. In his unconsciousness, he was trying to release the chakra when it got to dangerous levels, but the belt prevented this.
I had also planned for regular blue chakra to be a different type of radioactive decay than Kyuubi's red chakra. Alpha and beta are much more harmful to humans, so I was thinking that Kyuubi's would probably be this type and thus the reason it eats at Naruto's body if it lingers on him too long.
Now, it takes time to process chakra from the split of heavy particles, meaning it takes time for chakra stores to "refill." Naruto has abilities from Kyuubi to do this extremely fast. Sasuke's cursed seal allows him to do it faster than normal as well. Chouji's family makes more energy instantaneously by transferring body fat into energy.
3. Spiritual and Physical
The whole "chakra is a combining of spiritual and physical energies" thing is the shinobi explanation for "your individual capacity and body have to work in tandem for this to happen." By that I mean that your body will do all the work of splitting atoms unconsciously, but your ability to do it is based on your natural abilities, your spirit. This is why Sakura has lower chakra potential than Sasuke or Naruto: she is not genetically disposed to being a high chakra-output person, whereas Sasuke and Naruto are. Therefore, chakra is a combination of spiritual (genetic) and physical "energies."
4. Bloodlines
Clan Bloodline traits, like the Sharingan and Byakugan: what are they? Quite simply, they are the genetic work of a clan ancestor. A ninja can create a bloodline trait by going into their DNA and permanently manipulating their genetic code. The specific way it is manipulated will create the different results. It's a very complex process, with a high chance for failure and subsequent death or hideous mutation, and so is not done very often. But when done correctly, it can be passed down like normal genes (with some extra restrictions and rules), and so can become a bloodline trait.
5. Kyuubi and Kimimaru
Brian B said:
"I thought of Kabuto trying to cure Kimimaro's lung disease using transfered portions of Kyuubi's chakra from Naruto to slowly dissolve the corrupted tissue(If his lungs where what was actually wrong with him)."
My response:
The Kyuubi's chakra, if you could direct it like a laser, would be able to kill the bad cells in Kimimaro's lungs. The problem is that I don't think you could direct it like a laser, and there may be unforeseen complications with radioactive spread. Not to mention you might also have to cut the dead cells out afterwards and/or regrow the lost tissue, and that would create the same problem that Naruto and Tsunade face: shorter life spans of those cells. Each time a cell multiplies it runs the high risk of slight mutations in the genetic code. Thanks to this, our cells age, so we age. Since the rapid healing Naruto and Tsunade undergo causes their cells to multiply exponentially, the mutations build up fast and shorten the life span of the cells, and by proxy the life span of the person. Kimimaro would have this problem as well unless he got tissue transfer instead of tissue regrowth.
C. Shinobi Profiles
Subject A1: Rock Lee
Lee has almost no chakra because his "spirit" (genetic component) didn't dispose him to have much (see Chakra Explanations: Spiritual and Physical). Most of his abilities were already explained in the story already: chakra in the suit the Gai gave him keeps his cells from being harmed in the compacting process. It helps his body accept the changes. The chakra gates are rather like Naruto using Kyuubi: it's a sudden chakra potential epiphany—or, in other words, a sudden splitting of many atoms and therefore great increase in chakra output (and I mean a lot). It also involves a component of tricking the body into believing it's fine when it's not, rather like pain-killers. It's really akin to an adrenaline rush.
Psychology: Lee would throw the psychologists off for a while as well as stir many betting pools. Some would bet that he has a form of autism, others that he's just faking it, some that he has a mild form of mental retardation, and still others that he's bipolar. Eventually, it would be revealed that Lee is just a very, very optimistic person because he can't stand to think negative thoughts. Lee respects Gai because Gai is also very optimistic and real, just like Lee wants to be. After meeting Gai, Lee developed a strong desire to try his hardest to overcome his chakra disability through taijutsu. It would eventually be found that Lee is afraid to try new things not pertaining to his current taijutsu because he is afraid of failing, just like he did with ninjutsu and genjutsu. The therapy sessions would help him get over this fear enough so that when the shinobi return to Konoha, Lee asks Tenten to tutor him in weaponry.
Subject A2: Hatake Kakashi
Kakashi's reappearing mask act is a genjutsu. Though he is unconscious and has the chakra restraining belt on, the chakra line to his mask has already been set up in a constant flow. It would only falter after several days under the belt. The reason he can't use the Sharingan to its full potential is because he only has the eye and not any of the proper mental capacity to make it fully functional. Also, Kakashi's chakra wasn't made to make the switch between regular eye and Sharingan because he doesn't have the other Uchiha genetic components, so there's a permanent chakra connection to his eye. When it is not being used the chakra lies dormant and the Sharingan is blind, but while it is in use the pathway becomes active. That's why he has to cover it up: it would eat up his chakra. That's also why it doesn't disappear under the belt. Kakashi's silver/white hair is just an extra hair color that we don't have in our genetic codes in this world.
Psychology: As Kakashi is older and more experienced, the scientists wouldn't have gotten anything out of him--they wouldn't be able to draw up a profile because he simply wouldn't speak. If I were to personally give him a profile, I would say he probably has huge trust issues and learned from an early point in life that nothing lasts very long, esp. people, so it's better not to get too attached. He reads Icha Icha because he's trying to prevent himself from thinking too much, but he feels a certain compulsion to visit and honor the memorial stone in memory of the people he did know. His reason for lateness and laid-backness: partly as another way to prove to himself that he doesn't care about anything, but partly as a way to keep the memory of his fallen teammate, Obito, alive.
Subject A3: Aburame Shino
Shino has a symbiotic, mutualistic relationship with his bugs. The scientists compare his relationship to his bugs with the relationship that some ants have with fungus. The ants grow the fungus in their hills, feeding it and cultivating it, and then eat parts of it as their own food source (eating without killing). So in Shino, his bugs provide protection and obey his commands, he provides food and shelter. Since the bugs are put in Aburames from birth (with a few genetic manipulations to accommodate them), Shino's immune system would be very sketchy without his bugs present. His bugs are distantly related to the beetle family, but their digestive tract would be like nothing ever seen before. Their bodies are porous because they absorb and eat chakra directly through the skin, like frogs breathe through their skin.
Shino, ironically, would wind up having one of the best understandings of the scientists, and be the first to accept their help (see Basic Story Plot: The End).
Psychology: Shino would be rather a mystery for the scientists. He would have a strange point of view of the world because he communes with his bugs so often. He respects power and ability, but he also respects strength of character a lot because he doesn't feel he has a very strong personality. This is why he respects Naruto so much. As the scientists know how important Shino's bugs are to him, and taking them away would be the only way to get him on the path to "normality," they don't feel they're much they can do.
Subject A4: Tenten
Tenten would have been found to have a mild eye bloodline—a mild genetic change to her eyes that helps with depth perception and visuo-spatial skills, which explains her aiming accuracy.
Psychology: Tenten would have a very strong sense of self and ability. She would not allow the scientists to try to talk her into branching into areas outside of weaponry because she feels it is her strongest point and therefore the point she wants to focus on. She, like Lee, would have a certain fear of failure because she believes, like Neji, that there are some things you just can't control. Facing these issues would give her a connection to her teammates that would make their whole team work better together when they return to Konoha, and Tenten would trade weaponry lessons with Lee for lessons in Taijutsu (and they get to have a gushy teammate dialogue scene).
Subject A5: Nara Shikamaru
Shikamaru's shadow manipulation is merely a jutsu that his family created, and which they guard jealously. Anyone could learn it.
Psychology: Shikamaru would be discovered to be a genius and most of his laziness would be chalked up to boredom. A small part of his laziness would be explained by his mother's insistence on action throughout his life, and a slight mimicry of his father's laziness. Shia would take over his psychological therapy lessons and they would usually just play a game of shogi while playing word games with each other, trying to see what information they could trick out of the other. This would lead to a respect/hate relationship between them. The winner of the shogi games would always be Shikamaru, but he won't win all the verbal games.
Subject A6: Hyuuga Neji
The Byakugan is a result of genetic manipulations done by ancestors (see Chakra Explanations: Bloodlines).
Brian B asked:
"In the case of the Byakugan, I can see how it is very similar to the Sharingan and the recessive genes coming into play to activate it (see Subject A9: Uchiha Sasuke). But, how would you explain the near 360 degree vision without the eyes being on the sides of their heads like a spider or fish? I think I remember somewhere that mice or gerbils or some type of rodent can see almost all the way behind them even with their eyes being forward but the sight in their immediate front is hampered because of it. The loss of eyesight in the Byakugan is just above the vertebra with only a few degrees loss of sight at that. Now, in the anime, when activated all color is grayed, leading me to believe that their eyes no longer capture light but use some kind of x-ray echo location thing? X-ray is the only type of gray vision I can think of at the moment. I say echo location because x-rays still go in a straight line like light (right?) so the eyes would need a way to capture information from all around. Unless the eyes shoot the x-rays themselves, but wouldn't that develop cancer in their brains?"
My Response:
I'll admit that you thought about the Byakugan a lot more that I did. I kind of cheaped out on really complex explanations like that by going with the end-all answer: chakra can do anything if used correctly. It would be a manipulation of the chakra in the eyes that allows the Sharingan and the Byakugan to do exactly what it does. If you want to get more technical, like with your rodents, you could say that the changes to the genes (when it goes to recessive) are like nothing ever seen: those specific genes are completely unique. And they should be: they were made by someone's chakra. So they can do completely unique things, like have near 360 degree vision even though the eyes are in the front. I wasn't planning on getting really technical, but your x-ray vision explanation works well. And since x-rays use a type of decay energy, you could say that one of the alterations to Hyuugas is an immunity to that type of radioactive decay, so they wouldn't be harmed by it and could therefore shoot both shoot and receive it in the eyes. Oh, and x-rays and light doesn't exactly travel in a straight line—no particle does, because particles are always moving (we have not reached absolute zero yet!), but it's basically a straight line.
Psychology: Neji would be found to have an "external focus of control"--that is, he believes that an outside force controls the current of events in life, not your own actions. This viewpoint, as the psychologists would find out, has been undergoing a radical change of recent, thanks to Naruto. Neji's mind would still be on the tilt, trying to decide if he should believe what he has always believed or allow new evidence to change those beliefs. The scientists would be scrambling to allow him to make his own decision while keeping him hopeful for the future. Neji would be the closest to being considered suicidal. In the end, he would side with Naruto's point of view and find life easier to deal with afterwards, though he'd certainly have relapses into his old way of thinking.
Subject A7: Uzumaki Naruto
Naruto's abilities are explained earlier in Chakra Explanations: Specific Examples.
Kyuubi's store of chakra would be a separate, unique place in Naruto's body (not like normal chakra, which is dispersed fairly evenly throughout all the living cells in the body). It would be centered around the seal, but the seal would be something like a dimensional gateway (in the same family as the kind that Kakashi opened to bring them to our world). Depending on how closely Naruto is connected with the Kyuubi, the Kyuubi's chakra will appear and disappear in scannings. This will completely throw off the scientists. As with most chakra-related things, the seal reacts not only to Naruto's wishes but also to his emotions. Its strength in the beginning relied on the strength of will of the creator (the Fourth), but after a while that will begin to weaken and the seal would follow it. The Fourth would have pre-programmed the seal so that it would, after a certain amount of deterioration, alter so that its strength was linked to Naruto's will. His will to keep the Kyuubi imprisoned, or let him out, would then be the deciding factor in the seal's strength. This would explain why Naruto seems to have a harder and harder time suppressing the Kyuubi, and why it becomes harder to deny the more he uses it. This is also the area I have taken the most liberty in, esp. considering that I haven't kept up with new developments in the series. I've watched hardly any of Shippuden, though I've heard interesting things about it.
As a side note, some measurements and estimates I did based on a few episodes in the show lead me to guesstimate that Naruto has 10.8 times as much chakra as Sakura, 9 times as much as Sasuke, and 5 times as much as Kakashi—and all of that without the Kyuubi's influence. This is based on how many times Sasuke and Kakashi can do the Chidori in a day, and the chakra meter shown in one episode (I forget which; it's when Jiraiya starts training him, I think) that compares the amount of chakra Naruto uses to get the same results with bunshin as Sakura and Sasuke.
Psychology: Naruto would have a number of issues that the scientists would eventually realize were mislearned life lessons. As Naruto had no parents or guardians to teach him things, he would have a skewered point of view on many things. This would explain things like his blatant, unrepentant use of the Sexy no Jutsu, horrible eating habits, lack of an "indoor voice," and tendency to insult people through lack of tact. He would probably have a deep-seated desire for family and recognition, which is why he is so obsessed with keeping Sasuke, his first male friend his own age, around, why he is likewise obsessed with protecting his precious people, and why he wants to become Hokage (though part of the reason for that is also because he highly honors the third Hokage, who was the first person to show him kindness). For all his faults, Naruto would rate high on resiliency.
Subject A8: Yamanaka Ino
Ino's family manipulated their genetic codes. They have the ability to control their brain waves to an advanced extent, and to broadcast said brain waves (which usually remain in the brain) out of the body and into another body. When the seal to do the mind transfer/possession is used, Yamanakas can force their minds to be working with alpha, beta, and theta brain waves all in tandem, which are then sent out of the body and into the host brain. This leaves only delta brain waves (also known as deep sleep brain waves) in the Yamanaka mind, which is why they collapse unconscious. There would be an extra brain part to handle these complications, or at least more brain activity in certain parts of the brain: either way, Ino's CAT scans would show up different than mine or yours, or any of the other ninjas.
Psychology: Ino would get the general teenage girl talk—respect yourself, stop chasing after boys, etc. For more detail, see Shinobi Profiles: Haruno Sakura, subsection "Psychology."
Subject A9: Uchiha Sasuke
As outlined in Chakra Explanations: Bloodlines, Sasuke's Sharingan is a manipulation of his genetics.
To explain what is happening when Sasuke's eyes change from normal to Sharingan, and how it's inherited, here is a small excerpt that I had planned on having one of the scientists say: "It's as if the dominant trait is the one we see on the outside, but chakra can go into the DNA and change the phenotype to the recessive, which would be the red eye—except that when genes are passed on, the red is always delegated to recessive and has to be paired with a dominant. Two recessive just isn't possible. It might be sex-linked so that one gender passes on the dominant trait and the other passes on the recessive. Or it could be that anyone who ends up with two recessive traits is naturally aborted."
The Sharingan's mimicry of other techniques (to the point that it seems like they're reading your mind) is explained by the idea that the Sharingan works at speeds faster than light. Everything we see is only an afterimage, even if it is near-instantaneous. Those few pico-seconds it takes for the light to travel from point A (opponent) to point B (Sharingan user) would not exist when the Sharingan is active (it functions on a different plane than light, most likely dark matter), so the user would see the opponent's movement in real time and mimic it fast enough for it to look like they know what the other person is going to do before they do it. Uchihas would probably also have to manipulate the speed of the light when it goes back to the opponent (slowing it down) and speed their own reaction time. [Normal reaction time in humans is 1/4 of a second or so.] The actual copying is merely a mimicry of the hand seals and chakra output, facilitated by the speedy capabilities of the Sharingan. Anyone can do this, technically, if they can see chakra and watch the sequence of hand seals in a technique. It's just that the Sharingan allows Sasuke to do so on the spot instead of a gradual learning process.
The cursed seal on Sasuke's shoulder is a composite of foreign enzymes. Enzymes are catalysts for reactions (they don't alter the direction of chemical equilibrium; they merely speed up the reaction), and the ones in the cursed seal have a two-part purpose. 1. To speed up the splitting of atoms and subsequent energy regulation. (This is unhealthy for the body because it tires and injures the body with too much chakra.) 2. To alter the DNA in the surrounding cells so that they will most fully accept the enzymes. This alteration is what causes Sasuke's physical changes, and is painful and unhealthy since it messes amateur-ly with genetics (which can have serious repercussions). Thanks to a careful set up with chakra, the enzymes react to Sasuke's emotions and mentality, and Orochimaru, as the progenitor, can also cause a stir in them.
Psychology: As you probably guessed, Sasuke would be found to have serious psychological issues. He has trust issues and paranoia issues bordering on schizoid/paranoid personality disorder. But his drive and ambition to kill his brother would point more towards antisocial personality disorder. He would also be found to be asexual, though whether it's a symptom of a personality disorder of just his orientation would be unclear. Due to all of this, he would go under the heaviest therapy, and have the least success in bettering himself. On a positive note, when they return to Konoha, he would be affected by the changes the other characters undergo: he might respect some of their attempts to better themselves, and a bit of respect for his village and fellow shinobi is just what he needs.
Subject A10: Inuzuka Kiba
Kiba's genetic code would have come back with some dog genes (see Chakra Explanations: Bloodlines). This is fairly obvious to anyone who looks at him. Akamaru's genes, likewise, would have come back with some human genes, explaining his abnormal intelligence.
Psychology: Kiba would be found to be psychologically healthy, if a bit overly-competitive.
Subject A11: Hyuuga Hinata
The Byakugan is a result of genetic manipulations done by ancestors (see Chakra Explanations: Bloodlines). For more information on the Byakugan's specific mechanics, see Subject A6: Hyuuga Neji. Hinata's heart was healed with chakra, but it was done incompletely. This is why there is no surgery scarring and why her heart still acts up. In the course of the story, I had planned for the Medical team to do proper open heart surgery on her and so she would come back to Konoha good as new.
Psychology: Hinata's shyness would be blamed partly on personality, partly on losing her mother when she was young, partly on having a talented sister and cousin around her when she was growing up, and partly because of her father's strictness. Other than this shyness, which the psychologists would work on through various social exercises, she would be psychologically healthy.
Subject A12: Akimichi Chouji
For Chouji's chakra abilities, see Chakra Explanations: Specific Examples.
Psychology: Chouji would be found to have an insecurity about his weight, and a general fear that everyone will dislike him for it. This would clash with the ideas and pride that his parents raised him with: that his clan is supposed to be overweight for their pills to work and their true power to be known. It would be a minor thing that he probably would have worked out on his own as he grew up, but a few sessions of therapy would get him started on that path a bit sooner than in canon.
Subject A13: Haruno Sakura
Sakura's pink hair and Inner Sakura are explained by the same phenomenon: chimerism. Sakura is a chimera, which is a human with two different sets of DNA in their body. One way this can happen, and what happened to Sakura, is that she had a twin when in the womb, but the two embryos fused before differentiating too much. The dead twin's DNA makes up a large enough portion of her mind that it was able to develop a limited personality. It also resulted in her odd hair color—her hair is actually made up of a mixture of white and red strands that end up looking pink. Roans, a type of horse, have this exact hair color make-up.
As a side note, chimeras are actually quite common in the Naruto world because of all the manipulations that the shinobis do to their genetic codes.
Psychology: Sakura and Inner Sakura would have had the psychologists puzzling for quite a while. At first they would chalk it up to anger problems, but then they'd start thinking it was dissociative identity disorder (formerly known as multiple personality disorder), and finally they would do some readings of her brain tissue and discover her chimerism. From there, they would realize that she has an almost-other person within her mind. When they tell Sakura this, she would be rather freaked out at the idea that her not-twin is still with her in some way.
Sakura would also undergo the typical teenage girl therapy, the kind where they sit her down and slowly disillusion her beliefs in true love and shining princes in armor. She would be encouraged to continue her friendship with Ino, to try to be more independent from Sasuke and stop idolizing him, and to start looking at and recognizing the special qualities in other people besides Sasuke. She would also be encouraged to find a way to make herself stronger, since she has an insecurity about her strength. This would lead to Sakura asking Tsunade to tutor her in Medic-nin practices when they return to Konoha.