Later taking him to the misty lake, Kabuto conducted an experiment on Yūkimaru by forcibly releasing his chakra, partially calling forth the Three-Tails. Kabuto was satisfied with the results, and took an exhausted Yūkimaru to Yugakure to rest. There, Yūkimaru met Naruto Uzumaki, and they had a brief discussion about bonds. Soon afterwards, he was sent on a mission with Guren, but became sick along the way. Guren took care of him and they grew close, Guren reminding him of his mother. Guren gave him a crystallised camellia, telling him that it would never wither for as long as she was alive. Once he got better he ran into Naruto again, who offered to take Yūkimaru back to Konoha. Yūkimaru politely declined, as he felt his place was with Guren.
Later, Kabuto conducted another experiment with Yūkimaru; by consuming more pills than the first time, he was able to completely summon the Three-Tails. The strain caused his nose and ears to bleed, and he soon passed out, causing the beast to go on a rampage. When he woke up, he found Guren fighting the beast in order to protect him. Yūkimaru used his remaining strength to keep it away from her, but they were quickly washed away by the Three-Tails.
After recovering from the ordeal, Yūkimaru found Guren and Naruto arguing over him. Yūkimaru told Naruto that he was happy to have met him, because now he had a place to be: with Guren. When Guren engaged the Three-Tails again, Yūkimaru restrained it without the aid of Kabuto's pills for a short while. The beast escaped from his control, however, and Yūkimaru passed out. A group of Konoha ninja found and attended to him, and when he came to he told them that Guren and Naruto had been eaten by the Three-Tails. Yūkimaru helped them locate the beast and, after finding it, went to hide with Sai. He was quickly captured by Rinji.
Taking advantage of Yūkimaru's feelings for Guren, Rinji convinced Yūkimaru to take more of Kabuto's special pills and use his powers to control the Three-Tails. He used all of his strength to bring the Three-Tails to their location, and as he collapsed, he was caught by Guren. Rinji went on to inform Yūkimaru of the fact that Guren had killed his mother, something Guren admitted to. Yūkimaru was speechless, but Naruto interjected, speaking on behalf of Guren by telling Yūkimaru how much she had changed. While the past Guren had committed terrible sins, this Guren was regretful of her past transgressions. Guren added that, if he would allow it, she would protect him forever, to which Yūkimaru accepted.
Rinji attacked them, in doing so revealing himself as Kabuto. Kabuto explained what Guren and Yūkimaru's purpose was for the two of them to get close and become dear to one another so when Yūkimaru learned of Guren's murder of his mother, he would use his anger to make his power explode, although he was visibly surprised this hadn't occurred. He continued to speak about the violent future ahead for the entirety of the ninja world, and that being their reason for using Yūkimaru to gain the Three Tails.
While Naruto fought with Kabuto, Guren and Yūkimaru fled. Kabuto sent Rinji's reanimated corpse after them, so Guren defended Yūkimaru. When her Crystal Release attacks proved futile against Rinji's bats, Guren encased herself and Rinji in crystal, and they fell into the lake. Believing Guren to be dead, Yūkimaru let loose his power, driving the Three-Tails into a frenzy, and shattering the seal the Konoha ninja were very close to completing. Once the beast was driven off, Naruto found Yūkimaru, and brought him back to the other Konoha ninja to rest. Whilst there they discovered that his body had not been able to handle the strain, and he had lost his ability to control the Three-Tails.
Yūkimaru awakened to find the crystal Guren had given him fully repaired and glowing. He rushed off into the night to find her. Naruto, after realising he was gone, went to search for him but when he found Guren's crystal left in a patch of bushes, unblemished, he knew where Yūkimaru had gone, and decided to leave him be. He put forth this point to the rest of the Konoha ninja the following morning, deterring them from searching for Yūkimaru. As the Konoha ninja were leaving, Yūkimaru, alongside Guren and Gozu, looked down upon them, and Naruto saw them walk away. Yūkimaru was seen holding Guren's hand as they walked into the distance.
For an unknown reason, Yūkimaru has the ability to partially control the Three-Tails. By use of pills given to him by Kabuto, he can summon the Three-Tails. At first he could only make an apparition of the beast appear, after taking some of Kabuto's pills. Later, after taking a larger dosage of the pills, combined with Guren's Crystal Release, he is able to make the beast fully appear, but couldn't control it. Yūkimaru can also control the Three-Tails for a short while without the aid of Kabuto's pills, as when he restrained it when Guren was in danger of being harmed. When Guren seemingly sacrificed her life to save him, Yūkimaru lost control of himself and used his powers to the fullest which enhanced the Three-Tails strength and rampage enabling it to break through the Four-Corner Sealing Barrier. His abilities seem to be tied to his emotions.
Besides being able to control the Three-Tails, Yūkimaru can create a thick mist that completely envelopes the surrounding area, thus allowing him to slip away without the risk of being followed. It also enables the user and his comrades to attack unseen.
- Yūkimaru's favourite flowers are white camellias.
- Because of his connection to the Three-Tails, Yūkimaru is also believed to have some connection with its former jinchūriki, Yagura. The two also have similar appearances and both have an apparent connection to flowers, however, Yūkimaru is an anime-only character.
- Yamato referred to Yūkimaru's mysterious usefulness to Orochimaru as "the ability to synchronise with a Tailed Beast".
- In the omake at the end of Naruto: Shippūden episode 134, Yūkimaru made a cameo appearance along with Guren to commemorate the 350th episode.
- Yūkimaru, like his mother, is able to play the leaf flute. The song he plays is a song from the Naruto soundtrack called "Guren".
- (While picking up white camellias) "I like red camellias. I like white camellias. Camellias drop the entire flower, not just their petals. You can remove the oil from the flower, and the tree itself can be used to make ink."
- (To Sasuke) "I wonder where my home is. Is this where I'm supposed to return to? But something's not right. This is not the place where I'm supposed to return to. That's right… you wouldn't know that would you? Say, do you have somewhere to go back to? "
- (To Naruto) "So if somone is thinking about me, then that's the place I go?"
- (To Guren) "You're a nice person, Guren… you are the one I should return to, after all… and I'm the one you should return to, Guren. "
- (To Guren) "Uh-huh… and I will always think of you, Guren. For now and forever… and ever… I love you."