Okay, so first off Sakura is not a crossover with much of anything. She's a Gamer. She lives her life like a game system. But unlike most gamers she didn't get some MMO knock off, she got GURPS, which is probably the most exactingly detailed 'realistic' game system ever. It has precise rules for everything from starvation to technological development so it allows almost no 'cheating'.
When 'she' started the game at birth she was allowed to do Character Creation but it was made clear once that was done she would only progress via the normal rules for GURPS, which is fairly strick. You can't just buy unlimited ranks of Strength until you can punch down mountains without first buying a bunch of advantages that allow you to do so and you can only get those advantages at character generation. The problem is those all cost points she didn't have, so she had to go for the cheapest options and give herself a bunch of disadvantage to pay them off. The goal was to play the long game.
One trick GURPS has is its one of a few system that exactly codifies training. Two hundred hours of "training" equals one character point. But hours are not equal. Training with a true master (one who has a higher Skill than you and a good Teaching skill) counts double whereas self study counts half. "On the job" training counts at only one quarter the rate (ie if you work as a computer programmer you get one point in the skill every 800 hours you work).
Wanting to max skill acquisition Sakura did a few things to herself. She bought the cheapest but most wide "power acquisition" advantage; Magery which gave her access to all of the default Spells in GURPs. She also hoped to cheat the system by getting Qucik Gadgeteer which allowed her to build technology from the GURPS supplements; including the Biotech book for self augmentation, the Ultratech book for nanotech and hard light forcefield stuff and the Psi-Tech book for both genetic and mechanically augmented psychic powers. She also gave herself as many Compartmentalized Minds as she could afford, because every compartment can take separate mental actions and study is a mental action. So she could train at six times the standard rate (or one eight different things at once, anyway).
She also put points into an Ally; Anima Invictus which is an implant AI that gives her Mana Enhancer which raises the local Mana level for her and one yard/meter around her, reducing how much 'energy' spells take from her. And she bought a bunch of computer software as Signature Gear, including Tutorsoft programs that teach every skill and spell in GURPs as if she had a Master trainer for exactly one point in each, and virtual reality software and a complete set of every artistic work from her old world.
She also had a whole lot of disads including stuff like Terminally Ill and so on that really worried her parents at first. Because she could train so fast she learned Illusion spells first and used them to hide her various modifications from casual inspection and stuff like magical telekenisis to construct and charge up magic power sources and an extradimensional pocket she can go to and train and build in without being observed. She can use magic to conjure materials to build with.
Queue two and a half years old or so and she's nearing the end of her lifespan because of her disads. She managed to finish designing her racial template using her Quick Gadgeteer and design a magical ring that will instantly apply the template permanently (unless she wears the ting and wills it off). Her plans was to gain thousands of points worth of advantages and powers without having to 'train' them or needing the initial point investment involved. The 'system' messed with her, because it basically considered her in point debt from that body swap. So she needed to spend all that time as 'intensive training' to buy off all the points or she would have crippling pain. With the power of math this worked out to about three and a half years.
(Also at this time Sakura builds two more compartments into herself via wetware subpersonalities. One is Sakura Prime, who 'they' determined to grow up with a normal childhood. Two and half being about when a child starts to actually develop a personality. The other of which is a personality with Bloodlust and other negative mental disads that means it will go for the kill since Sakura knows she's a softy raised in a society where murder is not acceptable solutions and she needs to be able to 'pull the trigger' when it comes to certain assholes in the setting.)
She encountered Hizashi at this time and was, understandably, a little out of it at that point. Long story short, he decides to commit suicide. She decides this is dumb and narcs on him to Hiashi, who KOs Hizashi before her can go through with it. Sakura uses her knowledge of biotech to force grow a clone which they turn over to Cloud. Thus, the entire Hyuuga is in her debt. Hizashi goes into 'hiding' because Sakura uses an Illusion spell to conceal his Caged Bird Seal and he and Hiashi swap places every now and then. If people see two at once or in places they shouldn't be, well... shadow clones! Sakura also befriends Hinata and Neji and gives the former a boost of confidence and the later a kick in the teeth (it helps that Hizashi is, in fact, still alive and Sakura and Hiashi gave him a kick in the teeth as well). Sakura agreed to come up with a different solution to the Caged Bird Seal issue, a nanite colony in the body that would destroy the eyes of any Hyuuga who dies without having the side effects of making them into virtual slaves. She also provided them with nanosuit and hard light tech (Hinata survived the burial because she had on a nanosuit and a forcefield for the exam).
Working with Hiashi and Hizashi they devise The Plan. First, Hizashi remains in hiding to prevent Cloud spies from figuring out they have been duped. Also, this allows him to move around and accomplish feats such as allowing Hiashi to ambush Orochimaru when "he" was busy with the One Tail. The attack on Orochimaru mostly works out despite all the complications. (Orochimaru 'surviving' and everything that happened with Gaara and Ino were not part of The Plan, but they can be worked around.)
The next step of The Plan is to lure out Danzo by dangling the magic ring in front of him. With that ring he could create an army of super nin! The Plan is to make it seem as if Sakura is too connected to Hinata to resist if she is placed in danger, so Danzo would move to kidnap her and put her under his power to force Sakura to work for him. The hope is he'll move in a way that opens him to direct retaliation from the Hyuuga but Danzo is a clever bastard.
Danzo's plan is to trick the Sound, specifically the Sound Four(or Five with Kimimaru) to kidnap Hinata as part of a plan to get back at Hiashi for murdering their lord. Danzo then plans to intercept them at their hideout and take Hinata from them with his Root operatives and himself as trump card. Sakura and Team Kakashi (plus Neji, Lee and TenTen who were with them when the kidnapping happens) end up pursuing because Sakura has been released, Naruto et all have finished training and Sakura is the only one who knows Hinata has been kidnapped because of the transmitters in her gear. Queue running fights and stuff. Konoha uses this as an excuse to declare open war on Sound and sends a small army of jounin/Anbu to wipe out the village (including Hizashi posing as Hiashi and Might Guy).
Team Kakashi manages to defeat the Sound Five and a bunch of disguised Root operatives and get to Hinata but Danzo shows up at the last moment to take her. He unleashes Shinsui's eye on everyone there and rewrites their memories to make him a hero and convince them that Hinata is dead. This doesn't work on Sakura because her immunity to genjutsu. They fight but Sakura is at a disadvantage because everyone believes she's attacking Danzo for no reason.
Hiashi and Guy arrive by leaving the Anbu/Jounin behind to fight the Sound nin. Guy avoids being mindfucked because of his training to defeat the Sharingan but Hizashi does not. They fight. Queue Paragon Interupt as Hiashi comes out of nowhere and cold cocks Danzo, cutting off the power to Shinsui's eyes. He is forced to use the Caged Bird Seal to KO Hizashi, a process Sasuke sees through his Sharingan so he knows what is happening now.
Between Guy and Hiashi they put Danzo on the back foot enough he is forced to use Izanami. Sakura was waiting for this, despite her massive injuries from her fight she uses Control Illusion to seize his now Illusonary Body in place and then, before it wears off, she uses Dispel Illusion to dispel him.
RIP Danzo.
Unfortunately the rest of the Konoha forces arrive just in time to see her kill a trusted and revered elder ninja, and only two of the ones present could speak up for her. Everyone else, including her teammates are convinced she went over to Sound and assassinated him. Sakura is 'rescued' by Kabuto and declared Missing Nin.
"Just as planned," she says. After all, her Golden Ending isn't just for Konoha. She needs to save all the victims of Cloud, including Sasuke's squad, the test subjects and so on. With Kabuto's 'help' she can do that.
Back at Konoha the jig is up and Hizashi is forced to reveal all the backstory up above to Team Kakashi and the Hokage. Sakura is actually fine with this, as she has eliminated all the reprehensible elements of Konoha and now they can start working towards the Golden Future. She knows that Kabuto plans to betray her and try to dump Orochimaru into her body (by now, Kabuto has figured out that she is unaging and thus, the perfect body) or at least a body modified with one of her rings. She plans to use the ring Orochimaru has to lure in Sasori in three years (when Sasori think Kabuto will become his pawn again) and from there kill him and lure out Akatsuki. From there, she can lure out Black Zetsu and use an antimatter explosion to vaporise him. (She has access to various dimensional magic and tech that will hold him in place long enough if she can just get one shot at him. And if Obito needs to die alongside him, such is life.) From there, it's just moping up.
There is a complication, however. And it goes right back to Sakura's initial arrival in this world. You see, by making the decisions she did she didn't just alter herself. She altered the campaign setting. GURPS is a system about building towards any kind of setting, and the kind of setting is determined by the advantages the gamemaster allows. By selecting magery and high tech level and downloading the tutors on stuff like nanotech, reality travel, hard light, psychic powers and so on she was retroactively changing the world.
So it turns out History Has Changed. Thousands and thousands of years ago, long before Kaguya at the fruit of the scared tree, there was a precuesor civilization. Think Al-Hazard from Nanoha. They had plentiful magic, and sufficiently advanced tech that might as well be magic, and combined the two to rule the galaxy and nearby dimensions. Then Things Went Wrong.
In the default rules for Magic Sakura is using there is a 1 in 256 chance of a magical botch on any spell cast. Sakura normally avoids this because she got herself an advantage that allows her to reroll the outcome of a 'roll' for magic once per hour after it. If you critical fail, there is a 1 in 256 chance that the spell will summon a Demon, an extradimensional horror "sufficient to threaten the player."
The original civ fell apart when the existence of demons "sufficient to threaten the players" of people who casually terraformed planets and created pocket universes began to run amock. The only solution they could come up with was to destroy magic. So they went to every planet in their empire and planted a tree, a tree that would absorb all the mana in the world and render the location unsuitable for the existence of Demons. This, unfortunately, also destroyed their civilization which relied on magic as part of their infrastructure and they vanished into history, with only a few derelict habitats floating in space and/or the void between worlds.
And on this world, Kaguya fucked everything up by eating the forbidden fruit. This infused her with the 'purified' magical energy which is what became chakra, a power as potent as magic but without the possibility of summoning demons... because it made people into demons. This is why Kaguya went insane and ninshu fell apart and so much of the jutsu requires horrible sacrifices and terrible things to happen (seriously, why the hell does the sharingan require you to kill your best friend to evolve to mangekyo, that makes zero sense unless you presume a malicious deity behind it).
When Haguromo spread chakra among the people he wasn't just hoping to promote peace, he also wanted to eliminate the potential for Magic in the populace. Chakra nature devours and destroys magical potential. Effectively it removes Magery and replace it with a similar advantage called Chakra. This, by the way, is why 'natural chakra' can only be used by a select few Sages. Natural chakra isn't chakra, it's mana that has been slowly building up in the world since the chakra tree was sealed away in the moon. Normally the human chakra system purifies it and transform it into spiritual energy but if you overpower it the person is 'purified' by their chakra system. Sage Mode allows you to store mana and convert it into chakra safely to get a boost of having two game breaking rulesets at once in your favor.
This is also why Sage Mode is normally incompatible with Tailed Beast Chakra. Tailed Beasts are demons, the remain of demons absorbed by and digested by the chakra tree (ie, the Ten Tails). Haguromo split them up and gave them names because Names Mean Things to demons and he hoped they could overcome their nature of "opponents sufficient to threaten the magic user" and become helpful to mankind. (Things did not always work out as he intended.)
SO! Long story short, what Sakura did was turn herself into a throwback. She doesn't know it, but she is now a precursor human. The only one with the capacity for Magic rather than Chakra. This was all okay, until she was forced to use so much magic in her fight with Orochimaru. She was slinging more spells per second than ever before. So not only did she get that 1 in 256 chance, she got that 1 in 256 chance o f failing on her reroll and then her 1 in 256 chance of getting the worst botch result.
You see, remember that part where Naruto and Sasuke experienced each other emotions while under the effects of all Sakura's spells? That wasn't supposed to happen. That was her magic going chaotic. And when they all connected to the tailed beasts through Sasuke's genjutsu just as he ran out of chakra it created enough of a crack that a demon slipped through into the world, a demon "sufficient to challenge the caster" which is Sakura. It also supped a bit on the energy of Kurama and Shukaku so its more powerful now.
It takes on a human form and name, one taken from Sakura's memories of the "most reprehensible manipulative bastard in fiction". Hazama.
Though that isn't his real name or form. During the chapters leading up to the fight with Danzo it befriends Sasuke. After the battle, it approaches him and Sasuke it turns out Did Not Take Things Well. You see, he's smart enough to put two and two together. If Sakura knew the future and intervened to save Hizashi then she could have done the same and saved his entire clan. Further, without access to her power his progress is stymied and an encounter with Itachi convinces him he needs more strength. Enter Hazama.
One of the things GURPS demons can do is enter into contracts with people. The demon sets terms and in exchange the human gets the ability to use magic even if they don't have Magery. Turns out, Sasuke's Sharingan eyes are good enough to copy magic as well as jutsu and he witnessed Sakura's entire fight against Danzo and her teammates where she pulled out all the stops. The bad news for him? The more demonic power he draws on, the more he needs to as it diminishes her 'non demonic' powers. Hazama's goal is to have him interfere with Sakura and ensure that Kaguya gets reincarnated: because Hazama plans to destroy the chakra tree and release all restrictions on magic again so he and all his demon buddies can run amok.
Oh, and his true name is Nyarlathotep, so his buddies are bad news.
More bad news is that when Danzo fucked with Hizashi's head Hazama intefered and used his powers to erase all foreknowledge from him. (Something he blames on the genjutsu twisting his mind.)
Thankfully there are exactly two people who Sakura Told Everything to. The other one is well in place to secure the second part of her plan. The second one is Itachi.
So with access to Orochimaru's resources and with Itachi as a man on the inside working against him, the plan is to lure Black Zetsu into an inescapable ambush. Queue Sasuke showing up, seeing that Sakura and Itachi are working together and going fucking ballistic.
Sakura is caught completely off guard because she presumed Hizashi told him and the Hokage the truth (that was The Plan, after all). Sasuke puts his hand through her chest, rips her in two and goes after Itachi. Black Zetsu and Obito escape. Kabuto grabs half of Sakura's body and absconds with it. Kabuto, Zetsu, and Hazama trigger the Fourth Ninja War with the goal of becoming a demon god, releasing Kaguya and trapping everyone in Infinite Tsukiyomi and releasing the Old Ones and destroying the entire planet respectively.
Somewhere in here Naruto does his training to unlock Sage Mode and the Nine Tails Chakra Cloak.
Sakura is only saved from dying because Ino intervenes (Ino having been forced to go Missing Nin with her because she can't be more than 15 km from Sakura for three years). Naruto manages to intervene in the fight between Itachi and Sasuke long enough to space Itachi's life (Itachi was long ago cured of his illness by Sakura though he continued to fake it. Oh, and his degraded eyesight was fixed as well). Itachi serves as Nigel Exposition and tells what is going on and Sasuke and him kind of make up.
Sakura manages to repair herself and she, Naruto and Sasuke go to take out Kabuto before he can ressurrect all the dead ninja and, more importantly, Madara and his Rinnegan eyes that could lead to Kaguya being returned. Kabuto, however, used his DNA jutsu to absorb all "sakura's power" and is now a powerful mage on top of a broken ass villain. They manage to defeat him and Naruto convinces Sakura and Sasuke to spare his life. Good thing, because Kabuto was able to work out what Hazama actually is thanks to his experiments with magic (and Hazama trying to tempt him with power now that Sasuke has turned on him). He also points out that the only one with any hope of defeating Hazama is Naruto, who has gained the ability by combining Sage Mode and Nine Tails Cloak to purify mana into chakra and remove all the negative energy from it in the process. Because Naruto just rolls that way.
Sakura also reveals her trump card. See she reached the "peak" of her abilities way back when she fought Danzo. No amount of training will have a significant impact on her combat performance anymore, because that's just how GURPS works (she's bought all the skills and advantages she can, and higher skills). So in the time between her going Missing and the ambush of Zetsu she was busy playing Supreme Commander. Because she knew the Ninja War may still happen.
The coalition forces now have armaments from her extradimensional factory, so we have Ninjas With Magic Power Armor versus white zetsu and the undead. Hazama is okay with this because the more magic exists the stronger he gets (he taunts Sakura with this several times).
Going into endgame, Madara gets returned to life by Hazama instead of Kabuto (because he rolls that way). He also reveals that his contract with Sasuke allows him to control him and tries to use him to assassinate Naruto, since he knows Naruto is the only threat to his plans. They fight but Itachi intervenes and uses... some sharingan thing I forget but it allows you to force another sharingan to use Izanami. This turns Sasuke into an illusion and Sakura uses Control Illusion to purge the demonic taint from him. Itachi is out of the fight because he's blind now. That's okay, Sakura exists to pump up the heroes with mad support magic he doesn't need no demon shit anymore.
While they were distracted Madara completes his plan, becomes the ten tails jinchuriki and is promptly betrayed by Black Zetsu who resurrects Kaguya only for them both to be betrayed by Hazama who tainted Madara's body with demonic energy and things start ging straight to hell. He then reveals his true name and nature and the tentails/kaguya starts turning into a fetal Outer God that will devour the world.
Our heroes get a visitation from Haguromo who reveals that he tried to warn Sasuke about the demon when he felt it in their shared vision way back and he uses his powers to grant them both Six Paths Sage Chakra and all the bullshit that goes with it, oh and also to purify Sakura's mana so she is using chakra now (her powers remain intact) and gets awesome six paths sage chakra stuff of her own.
Our power trio confront Hazama/Nyarlathotep and Black Zetsu. Naruto defeats Hazama's physical form but Nyarlathotep combines with the fetal outer god. Sasuke defeats Black Zetsu who is also consumed in the aftermath. Our trio has no idea what to do about the god monsters but Ino (who is among the small group they saved) used her mad super telepathy skills (turns out psionic enhancement technology plus ninja telepathy powers combine really striongly) to reach out to the spirits of everyone in Tsukiyomo and connected them to Sakura, Naruto and Sasuke.
Via the Power of Friendship they purify all the mana in the world, banish the outer god and save the world.
The end.
