Some time after the events at Kannabi Bridge, Rin was kidnapped by Kirigakure and made the jinchūriki of Isobu in order to have her be rescued so the tailed beast could be let loose within Konoha. To ensure the plan's success, various jōnin and ANBU-level Kirigakure shinobi were sent to feign chasing them so that their return to the village would be hastened. Knowing this, Rin requested Kakashi to kill her to protect the village. Though Kakashi refused, Rin later intercepted Kakashi's Chidori, which was meant to hit a Kiri-nin, impaling herself on his hand. The Kiri-nin made an attempt to retrieve her corpse before leaving, but were stopped by an enraged Obito who had awoken his Mangekyō Sharingan after witnessing the events.
Since Rin's death, Kakashi would usually visit her grave, even sharing top-secret intel with her such as Naruto's birth as witnessed by Obito who had snuck back into the village in disguise.