So Long, and Thanks for All the Shadow Clones

Upon her return to the Hidden Leaf Village, Sakura settled back into her usual routine. She rarely went on missions any more— as one of the village's rare Iryō-nin, Tsunade found her to be of much greater use in the hospital rather than on the field, so she spent most of her time healing, learning to heal from Tsunade herself, and half-heartedly training the Lorentz Gun Jutsu with what little spare time she had.

Having sold Michiru's engagement ring, she now had more than enough money to buy the high-purity chakra metal she needed to begin practising Lightning Chakra Mode— though the process, which involved electroplating it onto her skin, sounded more than a little painful. The problem, however, was availability: there wasn't any on the open market, and she didn't trust the purity of what was being sold on the black market.

And so, Sakura went on with her life, one day at a time.

…

One fine August morning, Sakura was summoned by the Hokage on her way to work at Konoha General Hospital.

"I'm here, Lady Tsunade," asked Sakura respectfully, bowing slightly as she walked into the Hokage's office. "Is there something you need from me?"

"Do you still have that necklace I entrusted you with?" asked Tsunade pointedly.

Sakura nodded and reached into her deep cleavage, retrieving the First Hokage's jade necklace— a priceless relic that rarely saw the light of day any more. Everyone (besides Tsunade) who had ever worn it had met a tragic end, so naturally, Tsunade had entrusted it to Sakura for safekeeping. One day, when Sakura believed Naruto was truly worthy of the title of Hokage, she was meant to pass it on to him.

"What is this about, Lady Tsunade?" Sakura asked, dropping the necklace back where it belonged and casting a quick glance at Shizune— who promptly looked away.

"I've called you here to give you a chance to say your goodbyes," Tsunade began.

At that moment, Naruto, Sasuke and Kakashi entered the room, still slightly sweaty. They had obviously been training together before getting called to the Hokage's office.

"My goodbyes?" hiccupped Sakura in surprise. "Am I going somewhere?"

"Not you," said Tsunade gravely. "Naruto."

A shocked silence fell over the room.

In the original timeline, Naruto's main motivation to leave the village during the time skip was to get strong enough to force Sasuke to return, but having somehow prevented Sasuke's defection, Sakura hadn't expected Team Kakashi to be separated ever again…

"What are you talking about, Granny Tsunade?" said Naruto, his voice trembling slightly. "I don't wanna leave; the Leaf Village is my home, y'know?"

Tsunade opened her mouth to explain, but before she could get the chance, Jiraiya appeared on her desk in a puff of white smoke.

"Allow me, Tsunade," said Jiraiya, settling into the lotus position and making himself comfortable on Tsunade's desk. "Tell me, you two—" he looked at Sakura and Sasuke in turn, "— do you know what's sealed inside your friend's body?"

Sasuke had thought about it long and hard. How was it possible that a dunce like Naruto could catch up and overtake a genius such as himself so easily? The answer was that Naruto was cheating— he was using the chakra beast sealed within himself to fuel his techniques!

"It's the Nine-Tailed Fox that attacked the village around fourteen years ago, isn't it?" said Sasuke drily, glancing at Sakura— beneath all her quirks, he knew she was very smart, so he was certain she had already figured it out… even though in the original timeline, she had been among the last of the Konoha Eleven to find out.

"I've guessed as much," lied Sakura, who had known since the start. "And I think we all saw a glimpse of the fox when we used our Sharingan to stop Naruto's rampage."

Naruto was horrified when Jiraiya blurted out his most shameful secret in front of his friends, but then he realised that even though they had already guessed the truth by themselves, Sakura and Sasuke had never treated him any differently, filling his heart with warmth.

"There's an organisation out there made up entirely of S-ranked shinobi wearing black robes with red cloud patterns— the Akatsuki," Jiraiya continued. "For reasons we still don't fully understand, they're targeting Jinchūriki like Naruto. You've all already encountered some of them yourselves, so you must know just how powerful their members are, right?"

Sasuke clenched his fists until the whites of his knuckles showed. The image of his brother in those black-and-red robes was seared into his mind.

"So what?" hollered Naruto. "Sakura-chan beat them all easily! She made Sasuke's brother cream his pants, and she told me she turned that weird string dude into dust! And Shino's bugs ate that guy's friend alive! That doesn't mean I should run away from my home!"

"That's exactly the point!" shouted Tsunade, slamming her fist down on her desk. "You're not the one who defeated them, and Sakura won't always be there to save your sorry hide!"

"And those people you mentioned?" added Jiraiya grimly. "According to reports I've received, they're all still alive, somehow. They're all highly abnormal, and now, they know not to underestimate you all."

Sakura's jaw dropped open. She already knew Hidan had managed to survive as a skeleton, but Kakuzu!?

"How in the world did Kakuzu manage to come back from my Fire Style Rasengan!?" said Sakura, aghast. "I vaporised him! Did I miss one of his masks or something!?"

"Wait, did you just say Fire Style Rasengan?" gaped Jiraiya. "You improved the Fourth Hokage's Jutsu? How!?"

Too injured to write at the time, Sakura had dictated her mission report to Naruto, who had mistakenly separated her mention of Fire Style Rasengan into Fire Style Jutsu and Rasengan.

"Ahem," said Jiraiya sheepishly, as Tsunade coughed to get him back on track. "At any rate, Tsunade's right, you need to get stronger, Naruto… much stronger. As it is, you're not only a danger to those around you, but to the village as a whole. You wouldn't want to hurt your friends again, would you?"

Naruto hung his head in shame. Twice now, he had lost control and nearly killed Sakura.

"…Okay," said Naruto at last. "I'll go with you."

"Good, I'll make a fine shinobi out of you yet!" exclaimed Jiraiya. "Go and pack your bags, we'll be gone for a while…"

A year and a few months into her new life, Sakura realised that the time had finally come. The time skip was upon her… except that it wouldn't be a skip from her perspective. And so, Sakura, Sasuke and Kakashi accompanied Jiraiya to the village's gates and waited for Naruto to return from his apartment with his belongings.

"Well…" said Naruto hesitantly, as he reluctantly trudged up to them a dozen minutes later, carrying a heavy pack on his back, "I s'pose this is it, y'know? See ya…"

One by one, everyone came up to Naruto to say their goodbyes.

Kakashi went first, ruffling his hair affectionately and wishing him good luck.

"Heh, good riddance," Sasuke muttered, turning his back on Naruto— though it was obvious to everyone he didn't mean it. "Maybe now I'll finally get a chance to train in peace."

When it was her turn to say goodbye, Sakura couldn't hold back her tears. She threw her arms around Naruto, hugging him and pressing her chest against him. After everything they'd been through together, he was no longer just a character from her television screen— he had become a close friend she could trust with her life.

"Don't you dare come back without learning at least one new Jutsu!" Sakura sobbed, still clutching him tightly. "If you show up after two years having only figured out how to dispel Genjutsu, I swear I'll beat you so hard you'll wish you were never born!"

She discreetly slipped a pin-up picture of herself in the bikini she'd bought in the Land of Moon in his back pocket, just so he'd have something to 'remember' her by while he was gone.

"All right, that's quite enough," said Jiraiya soothingly, pulling away Naruto, who was also on the verge of tears. "Remember, Naruto… the only reason real men should cry is to shed tears of joy!"

And with that, Jiraiya and Naruto left through the village's gates. They turned for one last wave goodbye, before disappearing down the road.

"Sakura, your eyes…" said Sasuke hesitantly.

"What about 'em?" sniffled Sakura, rubbing her reddened eyes.

Her regular emerald eyes had turned crimson red by themselves, and where only one tomoe had once orbited her pupils in her irises, there was now a second…

"I think we're due for a training trip of our own, Sasuke. I'll ask Lady Tsunade for some time off," said Kakashi softly. "And Sakura… you should hurry back to the Hokage's residence. I think Lady Tsunade has something to tell you…"