He was not murdered, but rather sealed with the Demonic Statue of the Outer Path, into which Kaguya was transformed when Naruto and Sasuke utilized the combined sage technique. As the technique was being used to lock off the statue, Naruto noticed him trying to flee but arrested him and tossed him into the Chibaku Tensei. Zetsu attempted to kill himself by exploding, but he was stopped by Kakashi who realized what had happened.