In the time spent under Tsunade's eye, Sakura's skills as a healer improved. When she and Naruto had a rematch with Kakashi for the old bell test he used on them as Genin, Sakura revealed another surprise. She had also learned the secret to Tsunade's inhuman strength, splitting the ground beneath Kakashi. However, no sooner had the reunion happened, the three were issued with a mission to help retrieve Gaara from Akatsuki. After arriving at Suna, Sakura showed her growth by saving Kankurou from Sasori's poison.
It was here that their consultant Chiyo, a woman who had been heralded as a living legend, noted the similarities between Tsunade and Sakura. The trio and Chiyo set off in search of Gaara and his kidnappers. Along the way, their path was blocked by Itachi, the man to blame for Sasuke's attitude. Itachi put Naruto under a Genjutsu, which Sakura reversed, while Kakashi took Itachi on head to head. A two-sided attack from him and Naruto put Itachi down, only to reveal that it was not Itachi, merely a specially-transformed subordinate of Sasori, one of his partners in Akatsuki. The team, joined by a support group consisting of Gai, Lee, Tenten and Neji, broke into Akatsuki's hiding place and instantly began fighting. However, only Sasori and his partner, Deidara, were present physically. Deidara took off with Gaara while Sasori remained behind to deal with Chiyo and Sakura.
Sasori and Chiyo were both experts in using puppets as their attacking tools, with Sasori going one step further and hiding himself within the shell of one of his. With help from Chiyo, Sakura smashed open the puppet and revealed Sasori himself. However, this only served to raise the odds as he summoned another – the mutilated and mechanized corpse of the third Kazekage. In addition to the puppet modifications Sasori had made, the Kazekage retained his skills from his life, the ability to manipulate iron sand, which Sasori had mixed with his own lethal poisons. Chiyo responded by calling upon two puppets of her own – the mechanized remains of her own son and his wife – Sasori's parents.
The third Kazekage proved extremely difficult to neutralize, managing to inflict poisonous wounds as well as use the iron sand to disable the parental puppets. However, Sakura managed to pull off a last-second strike, shattering it to pieces. Sasori's next move was the biggest surprise of all. Pulling off his cloak, he stood on a cable with a spear-tipped end that coiled up into his stomach, with scythe-like claws sprouting from his back and other bodily augmentations – he was a living puppet himself. Chiyo drew her trump card, the White Secret Technique: the Chikamatsu puppet collection, a group of ten puppets controlled by one finger each. Sasori responded with his own, the Red Secret Technique and opened up a panel built into his chest. A hundred strings of chakra flowed out and connected to one puppet each, displaying his own collection of a hundred puppets, which he had used to conquer an entire country.
Although Chiyo's puppets were still quality over quantity, there was still too much risk and it was up to Sakura. With an item given to her by Chiyo, she managed to thrust at Sasori and trapped him up against a wall, sealing off his chakra. The puppets fell limp and Sasori's body with it. However, Sakura noticed at the last second that Sasori's body was empty – no eyes, hollow and lacking the small cylinder that had his name written on it. Before she could react, another puppet, now with Sasori's face and the missing cylinder, lunged at Chiyo. Sakura threw herself in front and took the fatal stab from the puppet's poisoned sword. Chiyo then quickly injected the last of the antidote into Sakura. Sasori drew back, pulling off the forearm section of the puppet to reveal another blade underneath. As he rushed forward for a second strike, he suddenly stopped as two swords impaled his body and the cylinder, critically injuring the last remaining organic part of Sasori. | Sasori gloated that not even medical techniques could heal the wound he dealt Sakura. Chiyo remarked that she was not using conventional medical treatment, but a method of life-force transfer that she had originally developed for Sasori that could even breathe life into a puppet. Sasori then realized that his dead parents could have been resurrected and simply muttered "pathetic", mocking the technique and questioning his grandmother's sanity. As the blood drained from his chest, he lost the ability to control his own body and finally dropped to the ground after he lectured Sakura on the advantages of his lack of morality and mortality, as well as leaving her a small hint before he lost consciousness, that he would be meeting with a spy he had placed among Orochimaru's underlings.
Meanwhile, Naruto and Kakashi had defeated Deidara and secured Gaara, who appeared dead. Chiyo transferred the last of her life-force into him, then told Sakura that she may well go on to surpass Tsunade. Shortly after, Sakura cradled her lifeless body as she passed on. As the leaf ninja left, Sakura brushed a hand over Chiyo's grave and said her final goodbyes.
No sooner had they got back home, things were already changing as her report on Sasori's spy prompted an investigation. Naruto and Sakura found themselves joined by two new faces – Kakashi's replacement as team leader, the man codenamed Yamato and the irritatingly blunt Sai, also a codename. The three met up with the spy, with Yamato disguising himself as Sasori. As a shock to them all, the spy was none other than Kabuto… however, Orochimaru himself had followed, surprising them both. Kabuto ran to "Sasori", but double-crossed him and slashed through him, revealing Yamato inside; unaware of what Sasori really looked like under the puppet.
Orochimaru told Kabuto that it was indeed a fake and invited Naruto, Sakura and Sai to step forward too. As Orochimaru's words drove Naruto into a frenzy, Sakura is knocked flat as a defensive outward burst of chakra from a Kyuubi-possessed Naruto and almost sent plummeting off the bridge, struck with a wound that proves difficult to close up. As Orochimaru and Naruto face off, Yamato takes measures to track Orochimaru, Kabuto and apparently, Sai. In the recovery time that follows, Sakura uses her medical skills to heal Naruto after his brutal Kyuubi rampage. Yamato takes the opportunity to address her not so hidden close feelings for Naruto. Sakura is taken aback by Yamato's view of her character. She doesn't get a chance to answer him though as Naruto regains consciousness.
The team then leaves in pursuit of their quarry. Despite a convincing dummy, the team fails to fall for a hung corpse mimicking Sai and presses further on, where they eventually end up inside one of Orochimaru's temporary bases. The team split up to search for clues, running into Sai's cell and apprehending Kabuto. However, the base is torn apart in a moment and Sakura finds herself staring up a cliff and into the face of Sasuke himself...
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