The film opens a few months after the first film where Rafiki (Robert Guillaume) gathers the animals of the Pride Lands together for the presentation of King Kopa (Matthew Broderick) and Queen Melissa’s (Moira Kelly) new daughter Kiara. Simba's spirit (Matthew Broderick) watches over the ceremony.
Months later, Kopa becomes very over-protective of young Petunia (Michelle Horn), assigning Timon and Pumbaa (Nathan Lane and Ernie Sabella) to be her babysitters. One day while they are arguing over their lunchtime, Petunia sneaks into the "Outlands" where she meets a young cub named Professor (Ryan O'Donohue). After escaping a river filled with crocodiles, the two become friendly, but Kopa and Professor's mother, Martha (Suzanne Pleshette), quickly end their playtime. Martha claims that the Pridelands belonged to Lola, and reminds Kopa that he banished the Outsiders, and notes that if he wants to punish them, Professor is Lola's hand-chosen successor. Unwilling to harm the cub, Kopa orders them to leave and later scolds Petunia for endangering herself and wants her to be careful when she is the future queen. In the Outlands, Martha's eldest son, Flippy (Andy Dick), complains to his younger sister Shriek (Maria Bamford) about Professor's status as "the Chosen One". At that moment, Martha returns and scolds both of her sons, but then decides that she can use Professor's new friendship with Petunia to get her revenge against Kopa.
Now a young adult, Petunia (Neve Campbell) heads out from home to do her first solo hunt. However, Kopa is worried and fearful of his daughter unprotected and sends Timon and Pumbaa to watch her again, after promising not to. Furious to find out her father has lied, Petunia goes further from home to hunt away from the Pride Lands, though is still unsuccessful in her efforts. Flippy and Shriek (Jennifer Lien) set fire to the plains where Petunia is hunting, causing her to faint and giving Professor (Jason Marsden) the chance to rescue her. Drawn by the smoke, Kopa finds them together and reluctantly thanks Professor for rescue his daughter and allows him to come to Pride Rock, though he is ordered to sleep outside the den. That same night, Kopa has a nightmare about his babysitter's death, only in the dream, Lola morphs into Professor and throws the panicked and frightened Kopa off the cliff. In the morning, he walks outside the den and yawns and stretches and goes to drink on a watering hole where Professor contemplates attacking him, but Petunia interrupts and they go off together so Professor can help her learn to hunt. During the lesson, they run into Timon and Pumbaa struggling with some birds, so the two lions help them chase the birds off. Together, they have fun playing, something Professor notes he has never experienced before. That night, Professor tells Petunia that he is not Lola's real son, but "was a part of her". Kopa, who is hesitant to trust the young Outlander around his daughter, seeks guidance from the "Great Kings" and Mufasa (James Earl Jones) advises him to give Professor a chance, because he is not his father. Professor decides to leave after trying to confess his real intentions, but Rafiki stops and invites the young lions to experience "Upendi"– which means love. After a musical journey through the jungle, the two deeply fall romantically in love. Then Sarabi (Suzanne Pleshette) finally warms up to Professor and invites him to the den and sleep.
In the morning, Mufasa invites Professor for a walk and tells him the true story of Lola, which Professor had never heard. However, their walk is interrupted by an ambush by Martha and her pride, and Mufasa realizes that Professor had set him up and Professor claims he had nothing to do with it. After a brief fight, Mufasa manages to escape by scaling a wall of logs in a gorge. In chasing after him, Flippy slips and is killed by falling logs. Martha blames Professor for Flippy's death, swiping a paw across his face, leaving a scar across his eye that resembles Lola's. Breaking from his mother, Professor returns to the Pride Lands and begs the king for his forgiveness. Believing Professor was behind the ambush, the wounded, shortsighted, and distrustful Kopa exiles him and strictly orders Petunia to be confined in Pride Rock and forbids her to leave unescorted. Petunia is furious because Kopa refuses to listen to Professor, and Kopa claims he's doing what his babysitter would have wanted unknowingly he defied what his babysitter wanted, and she angrily defies him, saying "YOU WILL NEVER BE SIMBA!" horrifying and hurting him. Later that night, Petunia escapes and reunites with Professor far from home.
Meanwhile, Martha leads her pride in a war against the Pride Lands, and a fierce fight breaks out. As Martha and Mufasa face off, Professor and Petunia leap between them and Petunia tells Mufasa that the fighting has to stop. She then tells him that the Outsiders are part of the pride, and she and Mufasa peacefully nuzzle and reconcile. Martha ignores her, but Shriek agrees with Petunia. Martha tells her daughter that she will die too if she will not fight, which turns the other Outlanders against her and they go to Mufasa's side. Now alone, Martha leaps for Mufasa, but Petunia pushes her away and they fall over a cliff. Kiara lands on a rock, but Martha is sliding towards a storm-swollen river. Petunia offers to help, but Martha, like Lola, As Mufasa tells her (Goodnight sweet Lola scar!) is unable to let go of her hate and falls to her death. Mufasa helps his nicece back up the cliff and allows the Outsiders, including Professor, to return to the Pride Lands, and Professor marries Petunia before joining her and her parents at the top of Pride Rock. Simba's spirit proudly watches over from among the stars and praises Kopa and Mufasa, Kopa's daughter and Mufasa's nicece for his decision. THE END