For the 2004 DVD release, Kovu's scream was reanimated into two frames
Kovu and Kiara return back to Pride Rock singing "Upendi" before it fades into the next shot. In the 2004 Special Edition release, the scene is edited slightly shorter than the 1998 print.
Rafiki's Introduction: After the main title, Rafiki is in his tree, drawing a picture of Kiara next to the old picture of Simba. A gust of wind announces Mufasa's presence and scatters the markings on the trunk, causing the "circle to break." Rafiki understands that there is trouble to come. He sees a new marking, made into the shape of a lion cub, Kovu. Rafiki realizes the cub is in the Outland, where Simba banished those loyal to Scar. This scene was not released in the original version.
Zira Trains Kovu: After Rafiki learns of the cub, we find Kovu pouncing on a bug. He laughs and lets it go. Zira scolds him and squashes the bug. She tells him not to be weak and reminds him that Scar chose him to be the next king. Then they would not live in the horrible Outlands. This scene was not included in the final version.
Zira's Suicide: An alternate version of Zira's death. Kiara attempts to reach Zira, but Zira smiles evilly at her. She says "No! Never!" and lets go of the rock, falling to her death.
Nuka's Death Scene, Extended: An extended scene to Nuka's death scene not in the final version. Zira cradles his face in her paw and Nuka manages to get out "Well, I finally got your attention, didn't I?" Zira smiles tenderly at him. "Didn't I?" Nuka managed to get out, then died.
Nuka and Vitani Bring News: Zira's older cubs race to tell Zira what they saw at Pride Rock, announcing Simba's cub is a girl. Zira laughs at this and says, "Scar, my beloved, this couldn't be more perfect." Nuka is confused at who his mother was talking to. Vitani said she was talking to Scar, and Nuka begins to act afraid. She reminds him that Scar was dead. Zira bitterly confirms it, saying if not for Simba, Scar would still be king and she would be his queen. Nuka tries to convience her that he should be king, but Zira snaps that they should respect Scar's "dying wish" and train Kovu to be King. This scene was not in the final version of the film.
Stinger: Showed after the credits that was not in the final version. Timon and Pumbaa are in the Outlands chowing down on bugs. Pumbaa shouts "Hakuna Matata!" Timon says "Outlands, shmoutlands... this place is better than Disneyland!" Then a bug flies into shot and flits from side to side like Tinker-Bell in the traditional Disney transition-out sequence.
When Kovu and Kiara are stargazing, Kovu had an alternate line, asking, "No one here thinks he's very great... do they?" after he asked if Scar was up among the stars. Now he says, "He wasn't my father, but he was still... part of me."
When Kovu begins to run away from the crocodiles, Kiara shouts, "What about me?!" Originally, he said, "You gotta take care of yourself!" Now he says "I'll distract 'em! Run!"
When Kiara runs away from Timon and Pumbaa on her first hunt, Timon says "Somebody's gotta get a beeper for this kid!" Originally in an alternate line, he says "Somebody's gotta tie a boomerang around her neck!"
After Kiara conviences Kovu to go back to the Pride Lands, Kovu says, "Race you back!" They both laugh and run off together. In the final version, there is no such line or scene.
When Kiara tells Simba that the Outlanders are the same as they were, she had an additional line removed from the final version: "Aren't we all part of the Circle of Life?"
During the Oulander/Pride Lander fight scene, Pumbaa asks Timon what happened to their old motto "Hakuna Matata." Timon replies, "Pumbaa, stop living in the past!" Directly after that line, he said "This is the sequel." That line was removed and went directly into the "new motto" line.
In the 1999 UK VHS and French versions of the movie, over the credits Tina Turner singing "He Lives in You" is played, instead of some instrumental music and "Love Will Find a Way".