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In the anime, a short while after the Five Kage Summit, Kabuto scrounged some of Hidan's DNA from the Nara Clan Forest. Not long after the massacre of the Tonika villagers, Kabuto confronted Naruto Uzumaki and Sakura Haruno, who were investigating the incident. Kabuto then used the The Hole's water and his snakes to recreate Hidan, whom he then took control of with a talisman. The newly-formed Hidan was then sent into battle against Team Kakashi on Kabuto's orders, after using a scroll to summon the original Hidan's scythe, which had also been salvaged. After a short fight, Kabuto retreated, having a snake ingest Clone-Hidan to transport him away. Later clothed in the attire of Kabuto and his reincarnated shinobi, Clone-Hidan's body remained dormant while Kabuto made adjustments to the technique.

The next day, Clone-Hidan, with his original self's personality recreated, along with a reincarnated Deidara, killed the Hachō Village guards who were guarding The Hole as a diversion for Kabuto to sneak into the village, a fact that greatly annoyed Clone-Hidan. The two began bickering about their respective defeats, which nearly escalated into a fight between them, when Yamato and Sai arrived with more Hachō guards. After a Tailed Beast Ball fired by a clone of Naruto detonated near the two, they were recalled by Kabuto, with Clone-Hidan being consumed by a snake once again, despite attempting to resist.

When the Ama no Hoko was activated, Kabuto's snake released Clone-Hidan to battle against the Konoha shinobi, at which point he found himself facing Team Asuma with a desire to enact his revenge on Shikamaru. Clone-Hidan managed to obtain some of the team members' blood from their battle and fled towards the Jashin symbol he had previously created above The Hole. However, Shikamaru restrained Clone-Hidan as his body began to break down due to the short lifespan of the snakes comprising him, ultimately resulting in the clone's death.