Kisame accompanied Itachi to Konoha to help kidnap Naruto Uzumaki. After the two gained attention due to their unusual clothing, they were stopped by Asuma Sarutobi and Kurenai Yuhi, two Konoha Jonin ordered by Kakashi Hatake to follow them. However, Asuma and Kurenai stood little chance, and were almost immediately defeated, until Kakashi Hatake arrived on time to save their lives. Kisame was able to distract Asuma While Itachi fought Kakashi. He waited patiently for Itachi's victory but before Itachi delivered the final blow, Kakashi remembered Jiraiya's warning, and recognized the duo as members of Akatsuki from their black cloaks. Itachi changed his mind, and ordered Kisame to kidnap Kakashi and kill Asuma and Kurenai. Fortunately, Might Guy showed up and kicked an attacking Kisame in the face (to which Kisame resents to this day). Following Guy's arrival, Itachi ordered Kisame to retreat, not wanting to start a large-scale battle. Kisame seemed quite annoyed with Itachi's idea though as he desperately wanted to fight the Konoha Shinobi.
Itachi and Kisame then continued to hunt Naruto, finding him under the protection of Jiraiya. After Itachi hypnotized a woman to distract Jiraiya and leave Naruto alone, Kisame and Itachi confronted Naruto in a hotel hallway. Kisame considered cutting off Naruto's legs so he could not run away, though Sasuke, Itachi's younger brother, showed up and drew their attention from Naruto. When Naruto attempted to fight, Kisame used Samehada to absorb all of Naruto's chakra. Kisame then attempted to cut off Naruto's arms so he wouldn't put up a fight. Before he could do this, however, Jiraiya arrived, and defended Naruto. Following the encounter, Kisame and Itachi were driven off by Jiraiya, failing in capturing Naruto.