During the second part of the manga, Itachi becomes involved in attacks to ninjas possessing tailed-beast creatures (Jinchuriki) until facing Sasuke in a one-on-one battle.

[18][19][20] In reality, as Shisui possesses the ability to subliminally manipulate others and shares Itachi's love for the village, he intended to use his gift on the Uchiha clan leader to stop the coup d'état.

However, Shisui is mortally wounded by the Leaf High Council member Danzo Shimura, who then takes his eye to achieve his own ideal of peace.

Meeting up with Konoha's Third Hokage Hiruzen Sarutobi, who promises to do what he can to look after Sasuke, Itachi reveals his intentions to continue to protect the village from the shadows.

[23] Itachi debuts in Part I after Hiruzen's death, when he uses his infiltration of Konoha to hunt down Naruto Uzumaki as an excuse to secretly check on Sasuke's wellbeing.

[24] After engaging with Kakashi Hatake and some of Konoha's forces, he reveals Akatsuki's goal to gather the Jinchuriki which are the people that contained the tailed beasts which there are nine of.

Itachi also learns that Naruto is under the protection of Jiraiya and sets up a trap to lure the experienced ninja away to grab the boy.

[26][27] In Part II, Itachi uses one of Sasori's informants as a clone of himself to hold off Naruto and the rest of his team while he and the others seal away Shukaku the One Tail.

[28] Itachi remains on the sidelines until learning that Sasuke has finally severed his ties to Orochimaru, having absorbed him and now being strong enough to settle matters.

[37][38][39] His soul beginning to fade, Itachi uses his Sharingan to project his memories to Sasuke to reveal the full story of the events leading to the Uchiha Clan Massacre.

[53][54] Itachi has ranked high in the Weekly Shonen Jump popularity polls for the series, continuously placing in the top 10.

[55] In the 2023 online global poll, held to celebrate the 20 years of the manga, Itachi was found to be the second most popular character in the franchise, behind only Minato Namikaze.

[56] The character received generally positive reviews from several publications for manga, anime, video games, and other related media.

IGN reader Jason Van Horn characterized Itachi as "badass" and jokingly mentioned that he is a character to be afraid of since, in his first fight in the series, he does not make any remarkable move.

[59] Activeanime writer Davey C. Jones celebrated Itachi's fights as the best ones in the series, noting his abilities to be as amazing as a "sci-fi ninja".

[64] Writer Jason Thompson highly praised his visual tortures, due to the effect it has on the victims, reminding him of the antagonist from Kiyoshi Kurosawa's film Cure notable for its horror scenes.

[66] Tejal Suhas Bagwe from Dissertation Submitted in Partial Fulfillment for the Degree of Masters of Arts in English describes the usage of god themed techniques within the Uchihas as major references to Japanese mythology especially when awakening the stronger Mangekyo Sharingan.

The contrasting relations between these two characters is a common theme within the manga, as not only this is explored through Naruto and Sasuke but also through the two other connected ninjas, Hashirama Senju and Madara Uchiha.