This is a Digimon and Naruto crossover fanfiction only, other characters and franchises may be included.
As fate would have it two of the perfect clones of Naruto and Sasuke apparently made it one dimension that was very much like their own except that when they arrived they found something rather odd, some of the people they knew actually were the opposite gender, Rock Lee, Neji, Kiba, and even Shikimaru were all girls, the two of them nearly caused their transfiguration technique to fail, they were laughing that hard.
They soon saw a calendar and remembered that this is the day when they both fought against each other in the valley of the end, and if things remain the same there might be a chance to stop the fight if they hurry, so they immediately took off towards the valley of the end, as fast as they could.
No matter how fast they went Sasuke had a feeling this was a fixed point in time so there was a chance that they wouldn't make it, and sure enough the Naruto and Sasuke of this dimension were doing exactly what they remember which was both nostalgic and embarrassing, that they ended up fighting in such a juvenile way. It is the reason that they wanted to stop it, this was one of the things they both regret doing.
As they saw the fight continue, Naruto was charging up a Rasengan and Sasuke of this dimension was charging up a Chidori, just like they remember doing except that unlike before this one was much more powerful than what they remembered doing, the minute the spinning ball of energy hit the lightning attack it was absorbed and caused it to turn completely black, injuring Sasuke to the point that he would surely die, and sucking in Naruto.
The attack was so powerful that it tore a hole in the barrier between dimensions and so which means Naruto was sent to another dimension that due to this one is now linked due to the breach of the barrier. They quickly did everything they could to stabilize and heal the Sasuke of the dimension they were in, but something felt off, and upon checking they found that indeed he had a seal on him to modify not only his memories but his body.
Going through the memories of this Sasuke they quickly saw that the Naruto that got sucked into that other dimension also had a seal on his back, it was the same kind that Sasuke had, so someone had to do this and it was clearly intentional, they both had one and only one suspect as they treated Sasuke who was injured badly enough that he was nearly dead.
Hiro looked at Hector who was looking like Sasuke, he let out a deep sigh, "You know who did this don't you? There aren't many seal masters that can do this in Konoha, Tsunade, Orochimaru, and Jiraiya could, but they wouldn't because for two the Naruto from here is their precious godson, and the other wouldn't because it might damage his precious little treasure."
Hector looked at Hiro who looked at Naruto and nodded his head, "True, it also gives a perfect chance to someone else to eliminate two clans from Konoha, and doing so means he could get himself and someone loyal to him a seat on the council, there is one that comes to mind, Danzo. He would do this if only to ensure that he can be a candidate to become the next Hokage."
They both agree that doing this was something so horrible that Danzo would do it in less time than a heartbeat if it benefits him. They did the best they could and decided to grab the body of Sasuke and take him back to Konoha since he needs medical attention and they need to establish a point of return if they want to be able to get Naruto and return him or her back to Konoha.
The two men walked towards the hospital and were alarmed and shocked at how the two men were carrying the last Uchiha in the village, at least that didn't change Hector under a transformation technique couldn't help but try not to laugh as they saw the medical staff treat this version of himself as the crown prince of the village.
They were quickly told to go and talk with the current Hokage and as soon as they made it to the Hokage Tower Hiro used a flight of the thunder god seal that he had on the bottom of his sandals to mark the place just outside of it as a place where he could use his father's technique and return.
With every step he took he marked the ground with a seal, they were both guided to the Hokage's office at the time it was a rather busty blonde woman sitting on the chair behind the desk, "Lady Hokage we have brought you the two young men that just brought a heavily injured and apparently horrifically mutilated Sasuke Uchiha, we came to deliver them to you and leave them for you to judge and punish." The ANBU who spoke was clearly a person that respected the Uchiha Clan quite a bit if the anger in his voice was any indication.
The ANBU left and both men decided to wait for permission to sit, "I want to know exactly how is it you found Sasuke and where is Naruto, I know for a fact that Naruto was tasked with the retrieval of his friend, he would not abandon this mission, so could you tell me that, but first sit down, and tell me who you are."
Hiro looked at her, almost feeling so happy to see her alive, that he had to fight back the tears as he restrained the urge to say to hell with the seat and go straight to hug her, instead he walked towards the chair, "I am Naruto Uzumaki, and my friend is Sasuke Uchiha but we are not from this dimension, we and thousands of our clones have been sent throughout the multiverse to help and improve the many dimensions in it."
Tsunade wanted to know that he was telling the truth, "Very well, the version of myself in this dimension does not know who his parents are, but I do. If you want proof, my father's picture is right next to Hiruzen Sarutobi, his name was Minato Namikaze my mother was the second Jinchuriki that held the nine tails, and descendant of the Kage from the village hidden in the whirlpool, Kushina Uzumaki. Do you want more proof? Should I tell you your actual age, the name of your lover, and brother, how much proof do you require of me Obaa-Hime. "
The young man sitting right next to him began to shake his head, "Naruto there is no need for insults, I am Sasuke Uchiha from his dimension, and we have many important things to talk about. We know where to find them because we fought each other in that same valley in our dimension, We are also not the same as them, we may look young, but that is simply due to the effects of traveling through dimensions, we are both Jounin, in fact, impressions and insults aside Naruto later became Hokage himself."
He heard a person scoff at the very idea that Naruto ever became a Jounin and laughed at the notion that he would be good enough to be Hokage, immediately Sasuke threw a Senbon needle at the person who was hiding and pinned him against the wall behind him. "I would watch what you say about my friend, I will not have a person who is trying to listen to a private conversation insult my friend, so take a hint and leave the room or so help me, I will make you."
Tsunade saw that this is not an empty threat seeing what she saw in the eyes of the black-haired young man was not a Sharingan but something that made even her afraid, the dreaded Rinne Sharingan. With a move of her hand, those ninjas that were hiding to protect her exited the room. He was not lying, he was no Genin, and being able to detect ANBU who are experts in stealth is a clear indication he was telling the truth.
"So you are a Naruto and Sasuke from another dimension, please tell me why did you bring Sasuke back, and what happened out there. Where is the Naruto from our dimension, would you kindly please tell me that." Sasuke couldn't leave this up to Naruto knowing how he would answer, "The attack that they did cause a breach in the dimensional barrier, which sadly means that where your Naruto ended up is now permanently connected to this dimension, and also connected to every other dimension that is connected to that one. As for why he returned with him, simple, he wanted this Sasuke to get the best medical treatment and the only person who can do that is you."
He looked around and saw that not much has changed in the old office, "As to what we discovered, apparently someone slapped a seal on your Sasuke to turn her into a guy, and another one to turn Naruto into a girl, we can only speculate but we came to believe it was Kurama that kept the seal from activating, but due to the effects of dimensional energy on the seal, and should Kurama no longer be able to prevent the seal from activating, once the seal activates your Naruto will change permanently from a boy into a girl."
His friend was glaring daggers at him for saying that, but it had to be said, "Thanks a lot teme, as I needed you to remind me of the fact that I in this dimension could in fact end up as a girl, I remind you that you in this dimension also was one, no cause I am not going to be mean to you like that, instead we should focus on the important things such as why Sasuke of this dimension needs to go to Orochimaru to train under him and convince him why he should return as a new ally of Konoha."
Tsunade was caught off guard by the comment by Naruto before her, why would he want to have Orochimaru the worst traitor to Konoha become an ally of it, Orochimaru is obsessed with destroying the village, there is no chance that he would suddenly decide to give up on his old grudges and return to Konoha as an ally. "He killed the Third Hokage, he wanted to destroy this village, and tricked our allies to help him do it, what makes you think Orochimaru would ever do that? If I agree to this, it is practically a suicide mission."
Sasuke looked at her and began to shake his head, "Because in our dimension Orochimaru became an ally to Konoha, in fact, he has told me that had he done that sooner, his medical research alone could have saved many of our forces and he still regrets that. I was his student I would know."
Tsunade then asked him if he had any other students, to which he did mention a rather surly senior student that went by the name of Kabuto, actually, Sasuke always had a tough time getting along with him, so might make things easier if they tell Sasuke from their dimension to try and be more sociable. Naruto said that was the pot calling the kettle black, which earned him a cold glare.
"So having him basically come to terms with what caused his grudge and have him realize that he can do much better for himself and Konoha by returning as an ally? How? Both Jiraiya and I have been trying to do that for years, and yes it has taken us a long time, but let's face it being a single mother of three is never easy."
Naruto hearing this freaks out, "What do you mean single mother of three? Where did those kids come from? Why, no better how?" Tsunade was rather shocked after hearing his little outburst. Tsunade simply looked at him and told him that if he must know, she and Jiraiya had a little too much to drink one night, which ended up with two things happening, a one-night stand and a pregnancy resulting in triplets.
"Well it was better than what happened to me, one minute I am treated like royalty, I could do no wrong, and then I do something stupid as most kids do something absolutely stupid, and much like that it was something I regretted even now, the girl who once exclaimed her never-ending love for me, took my blood, my very DNA and with the help of a cousin, made herself pregnant and then I had a child I didn't even have a hand in conceiving and met her when she was practically a teen. If my life is filled with anything these days is loss, grief, and regret. And so here I am trying to prevent that to happen to your Sasuke, so she might have a better life than mine."
Tsunade looked at the guy who told her he was Sasuke and he sort of looked like him, but as she looked she saw the sadness, bitterness, and anger in his eyes, what should be red when his eyes were active was a much darker color almost cold. Orochimaru would be amazed but Sasuke had a pair of Rinne Sharingans, the rings encircled the tomoe in both of his eyes, but there was no joy in them.
"So trust me Tsunade when we say this dimension is different than ours, in ours you and Jiraiya never had any children. In fact, both you and Jiraiya died alone in a most tragic manner, as to what we are doing here, we are waiting for you to send for Jiraiya to have him undo the seal, and thus restore your Sasuke as she was supposed to be, we suspect Danzo was the one that had someone place that seal on her, it must have been done when she had a physical exam at some point, it is a rather complex seal."
That is when she decided to ask if they could see and understand the purpose of the seal couldn't they remove it, and Naruto told her that yes he could, but had he done this before returning her back to the village it would have caused all sorts of trouble, first, they would assume the worst and that would not end well, and second, it would harm Sasuke.
So instead of healing her and undoing the seal sending her off to Orochimaru who she was going to for training to become strong enough to kill her brother, Naruto figured that it would be better that it was a secret mission, that way when he returns he didn't abandon the village as much as he is simply returning from a long term mission. This would harm Sasuke less and maybe just maybe allow Sasuke the chance to rebuild her clan.
As for Naruto as soon as Jiraiya removes the seal and that is taken care of, both of them plan to track the energy of the Kyubi from their dimension and maybe find a way to get Naruto back to Konoha, it was not pleasant but he did mention that ending up getting their gender-swapped while traveling between dimensions did occur. The only reason they could do it is that technically they are not mortals and have a great deal of experience in traveling between dimensions.
"So you are saying the Naruto that we think as a boy could end up returning as a girl, and there is nothing you can do about it. Well, I can tell you this, if that happens and you return with her, I want both of you to come and have a drink with me because that is the only way I can excuse myself for laughing my ass off." Sasuke told her that they can do that, and he would do better, when he is in that other dimension where Naruto ended up, he would try to buy the liquor for their little drinking party.
Why would he do that Tsunade asked, Sasuke simply laugh as he looked at Naruto scowling, and said that he will be the only one that will be able to since Naruto will be furious about this, he has ended up as a girl couple of times and he even managed to defend and save a couple of dimensions only because he could turn into a girl, Sasuke could never understand why this upset him so much when he was the one that invented the deadly and shocking technique that he called the Sexy Jutsu.
Tsunade had to agree that the technique he mentioned was in fact deadly, but having it be invented by a student in the Academy while he wasn't even a Genin was even more shocking once she found out, it would mean Naruto had knowledge of female anatomy and physical language, which may even include reactions to stimuli that went beyond of what a student, a boy should know.
"All this talk let me think there might be some reason to think that he knows girls far better than most expect, or worse he knew the shadow clone technique before people even heard of it and used that to make a clone of himself, then had that clone turn into a girl to learn what he needed."
Sasuke told her that according to what they saw in the memories of Sasuke from her dimension it could also mean that this information was implanted into the person as part of the seal. Seals are far more flexible and versatile than people give them credit for. A single piece of paper can store the furniture of an entire house, set a building on fire, cause a tidal wave to demolish one, or even a gust that could uproot from its very foundations all with a few pieces of paper.
As they told her everything she decided to have Jiraiya go to the hospital and have a look at the supposed seal on the back of Sasuke Uchiha, the one that these two men brought back to the village, she believed that everything they said is true and as crazy as it sounds that there is now an opening to another dimension that links theirs to the other one everything they said so far made sense, but a little confirmation never hurts.
As Jiraiya was told he went to the hospital and asked to be able to examine Sasuke by himself, and sure enough as he was told an elaborate seal was present on the back of the young man, it was done in such a way that if the person didn't know about seals they would never notice them. Having Minato as his student however and what he invented gave him more knowledge about seals than most would suspect.
The seal was something that was doing something to the body of the target, but so far he could see physical, mental, and memory seals as part of it, it was complex and it seemed to also a complex method of activation. The only thing he could think to do was to remove the seal and place it on a sheet of paper so that he could spend more time studying it later.
The seal would not be destroyed it would be removed and as such, it would deactivate on the person but still leave the seal intact and complete on a sheet of paper. This is probably how they placed the seal in the first place, they made the seal on a piece of paper and transfer it from the paper to the back Sasuke by using Chakra and pressing the paper on his back.
As soon as he did place the paper on Sasuke's back and fed it some chakra in the way he thinks it was done to apply it the seal came off, and it was perfectly intact on the piece of paper, except the minute he did Sasuke's body began to bulge and contort like his body was nothing more than clay and some unseen hand was molding it. The entire process was extremely painful from the way the young man was screaming and begging for it to stop.
Ten minutes of anguish, tears, and screams later and the form of Sasuke finally finished changing into an athletic and curvy young woman, the fact that was not wearing anything on her upper body gave Jiraiya while unintentional many glimpses of her figure, and he had to admit while being just a teen she had a nice body and given a few years and some work could turn out to be quite the beauty.
Sasuke was more concerned with the fact that in a matter of less than an hour he went from being a boy to being a girl, and Sasuke had no clue what the hell was going on. She of course was doing exactly as any young woman would do in this situation, freaking the hell out.
"Sasuke I understand that you are upset but I need to ask you about something, I did nothing to you, the only thing I did was remove a seal that two men who brought you back to the village told me they saw on your back, but I must ask you this, why would you ever consider leaving the village and going to learn from Orochimaru?"
Sasuke was in tears, she said it was the only way she could get strong enough to avenge her dead parents, and having to fight Itachi who was a prodigy and an ANBU Captain at the age when Sasuke herself was only a Genin made her realize that training under a Sennin would be the only way, and Orochimaru offered that to him once.
Jiraiya told Sasuke that he doesn't trust Orochimaru, even less so after he killed their teacher, but as the two who brought him back to the village talked with the Hokage, they said that they may have a mission for her that could in fact grant him the training she desired and be able to be of service to the village at the same time.
Sasuke told him that she would need a reason why would she accept a mission that was caused or implemented due to two strangers that she didn't even know, Jiraiya told him they said that she would say something like that, and in fact, they could sweeten the deal as it were, her bonus for doing as she was asked was the absolute truth behind the Uchiha Massacre, the whole truth and nothing but the truth.
That was the only thing she needed to hear, these two know what really happened on that day and who is behind it, she was now more than willing to at least listen to anything they had to say, who knows they might actually make good enough allies to help her against her big brother and achieve one of her goals, to avenge the death of her parents. Now the only problem was that she needed something to wear cause she couldn't walk around wearing a hospital robe.
She immediately asked a nurse nearby if she could buy some clothes for her, and sure enough, the nurse told her that the hospital actually has a room full of spare and discarded clothes ninjas of the village could use in case of emergencies. Well after she got dressed in some clothes that she remembered Sakura once wore, and the lesson on how to strap on a bra from the person Naruto called the Pervy Sage, suddenly the nickname seemed appropriate.
The two of them walked towards the Hokage Tower where they would meet the two men who brought her back to the village, somehow hearing that they knew what she really wanted to know motivated her to use Chakra through her legs so the one that had to keep up was Jiraiya some would say she was walking very fast, but Jiraiya was running after her, so to him, they were running towards the tower.
They finally made it to the tower and walked all the way to the massive door that leads to the Hokage's office, they knocked on it and heard a woman telling them to enter, the minute they entered Sasuke ran towards the guy who looked exactly how she remembered she had looked like before she had that fight against Naruto. The thing is besides that as she thought that she wondered where the hell is Naruto, and since he was not present she began to fear that she really did kill her best friend.
That is when the one that she was standing in front of finally spoke, "Relax, I know your memories are still a mess due to that nasty seal, so I don't hold it against you that you are shocked to see me look like this, but there is a perfectly rational explanation, I am you from another dimension, now come over here and sit on the chair that is right next to the Pervy Sage."
Jiraiya was indignant about the way the guy who says he is Sasuke from another dimension talked about him, until the very same young man told him that unless he wanted him to tell Tsunade what exactly he has been doing while supposedly running his information network he should watch what he says or thinks, or he might live to regret it. The young man's normal black eyes turned golden with the slit of a serpent on them.
"So where did you learn that intimidation technique from?" The now female Sasuke asked her the guy who looked like she did before, Sasuke told her that it wasn't anything outlandish Manda was many things but not many knew how an excellent teacher he can be if he is shown the proper respect. Sasuke even told her that he mastered the snake sage arts as such he was considered a sage of the Ryuchi cave. The Naruto next to him however was a sage of mount Myoboku.
This caused Jiraiya quite the shock that he could enter partially into a sage mode with such ease, "As you might be wondering Sasuke after talking with these two men I am giving you a secret mission, to go to Orochimaru and accept his offer to train you, but while he does slowly convince him that it would be better for him to let go of his grudges and to become allies with Konoha. Don't worry I will give you a scroll with all the relevant information you need to know and once you know it, you can just use Chakra to cause the scroll to burn."
"As for why? Let's just say that according to what I am told, this will make it harder for the one that truly was behind the death of your parents to hide, you see he is counting on Orochimaru to draw away the focus of everyone so he can do as he wants without anyone noticing, but if he doesn't have that distraction, he will have a much harder time to do anything now won't he?"
Sasuke not wanting to hear anything more asked who was responsible for the death of her parents, the one that looked like Naruto decided to answer since she will not listen until she hears what she wants, he knows how stubborn she can be so he had to tell her. "His name is Danzo Shimura, the man who is not only responsible for the death of your parents but also the death of all those other Uchiha with the aid of a rogue ninja he didn't know was helping him. The Hokage wants proof the real reason that he bandaged his arm and face is simple, he stole the eyes of the dead Uchiha and grafted them into his arm and face, he can't remove them without dying and he even pillaged the grave of the first Hokage to be able to do this, Orochimaru was paid by him to do the operation."
That is when she told him that is impossible, he was a member of the Third Hokage's council, one of his most trusted advisors, and she remembers that Itachi was the one that killed her mother and father, to which Naruto told her he did, but only after Danzo threatened that his sister wouldn't survive if he didn't do as Danzo told him to do, so basically Itachi was forced to kill his own parents just because he loved his sibling that much.