He is the primary villain in the sequel The Return of Jafar. After Iago is able to get the lamp out of the Cave of Wonders, he abandons Jafar and drops his lamp into a well. The lamp is discovered by the dimwitted bandit, Abis Mal. Abis Mal technically becomes Jafar's master because of this, but Jafar takes command of Abis Mal with a combination of intimidating the incompetent thief (though he does take human form to avoid scaring Abis Mal more than he needed) and their mutual hatred for Aladdin. Abis Mal takes Jafar to Agrabah after botching up his first two wishes and follows Jafar's orders to not only kill Aladdin, but emotionally destroy the boy as well. Jafar enslaves Iago and forces him to help capture Jasmine and the Sultan. Jafar also captures the Genie and Abu to make sure they don't interfere. After capturing the Sultan, Jafar slashes the Sultan's hat and takes Jasmine's form to frame Aladdin for the Sultan's "murder". Before he goes through with his plan, he does show admiration for Jasmine's spirit, implying that once he takes over Agrabah, he'd try to make her his queen again.
Aladdin gets framed for the Sultan's "murder" and Aladdin is devastated when "Jasmine" accuses him. However, Iago turns on Jafar and rescues the Genie. Before Aladdin is executed, Jafar reveals himself to Aladdin and leaves. The Genie arrives in time and saves Aladdin and his friends tell him that Iago was on his side. Now that they know Jafar is back, the Genie explains that since Jafar is a slave to the lamp, the lamp's destruction would kill him. The make it to the throne room where Jafar starts threatening Abis Mal to free him of the lamp and even resorts to bribing Abis Mal to make him grant freedom. When Abis Mal questions Jafar, Jafar threatens to make Abis Mal suffer since he can't kill anyone though "You'd be surprised what you can live through!"
Jafar sees Aladdin and attacks the boy with a fireball and transforms into his genie form and opens up the earth, allowing lava to flow. Aladdin gets trapped and while Jafar gloats, Iago attacks Jafar who hits the bird with a fireball. Iago lands next to Jafar's lamp and with his last ounce of strength, Iago knocks the lamp in the lava. The lamp melts, killing Jafar.