During the Third Shinobi World War, Team Minato was assigned to destroy the Kannabi Bridge. During the mission, Rin was kidnapped by Taiseki during the course of the mission, and Kakkō — another one of her captors — attempted to interrogate her using genjutsu to find out if she knew anything about Konoha's war efforts. Rin's will, however, proved too strong and did not break even under the genjutsu.
She was later rescued by Kakashi and Obito. Although they succeeded in rescuing her, Obito was crushed in a cave-in caused by Kakkō. Before Obito "died" however, he asked Rin to implant his Sharingan into Kakashi's left eye socket to replace the latter's damaged one. Wasting no time given the very grim circumstances, Rin began the procedure immediately, after which, she and Kakashi were forced to flee when enemy reinforcements arrived and continued the cave-in. Minato would later arrive on the scene and defeat the Iwa-nin. After Kakashi had recovered, the team went on to complete their mission and destroy the bridge. In the anime, it was shown that Rin was sent out on a mission with Kakashi and Guy. With their situation looking grim, Guy used himself as a decoy to lead away the Iwagakure shinobi, and Kakashi went after him. Rin later returned with backup from Konoha, which caused the enemy-nin to retreat.