In the beginning of this film, Leo is an adult and has just learned that his mate, Lyra, has just given birth to twin cubs: Lune (pronounced Lu-Ney) and Lukio. After a grand celebration, the scene changes drastically to a bustling city where a man named Ham Egg is travelling from jeweler to jeweler to try and sell a special stone he found in the Bajalu Jungle. After being turned down at every pawn shop and jeweler he goes to, the jewelers all inform someone of Ham Egg's whereabouts, and soon he is hauled away in a black car by intimidating men in black suits.
As it turns out, the stone that he's been trying to sell is really the "Moonlight Stone", a mineral that could be used as a power source and save the world from an impending energy crisis. A scientific organization led by Dr. Plus and Dr. Minus seek the help of Ham Egg to lead them to the source of the Moonlight Stone so it can be salvaged and used to help humanity. Ham Egg, however, is only interested in money, but is soon persuaded by Dr. Plus who is well aware of Ham Egg's illegal poaching activities. Ham Egg agrees to work for them, but demands to be put in charge of the search. Accompanying Ham Egg is Mr. Lemonade of the organization, and Dr. Moustache who is already stationed in the jungle.
When they arrive in the jungle, Dr. Moustache and Mr. Lemonade are shocked by Ham Egg and his "friends" who want only destroy jungle forest land and shoot any animal they come across. Dr. Moustache constantly argues with them over being respectful to nature, as Mr. Lemonade records everything that happens in his journal.
As Leo's son, Lune, becomes more and more curious of the human world, Leo continues to protect the animals of the jungle from whatever may threaten them, including Ham Egg's sinister actions, dissent amongst the animals, and a deadly disease that is affecting the animals.
With his domain violated by humans in a relentless search for the Moonlight Stone, their actions bring death to the jungle and break up Leo's family. Leaving Leo with the heavy responsibility of bringing peace to the jungle, his family, and even the humans.
Lune leaves the jungle behind, and travels by a log in the water to a nearby city. Lune is found by fishers and taken to a circus. A girl from the circus decides to take care of him, and he befriends a rat named Jack. Eventually a bird from the jungle finds Lune and tells him of how the disease is killing off many animals and she leaves with her flock. Lune is frightened by the idea that his family may be dead. Eventually there is a fire in the circus and Lune gets all the animals to help put it out. Lune, Jack and, the girl who took care of Lune bid their goodbyes and Lune sneaks onto a boat that will help him get back to Africa. In the jungle, Lyra is affected by the deadly disease and shortly dies. Although Lukio comes down with the same ailment, Dr. Moustache is able to cure her. We see near the end of the film that she gets better. However, we do not see her in the rest of the film.
Leo, heartbroken by the disintegration of his family, decides to lead the humans to the center of the mountain where there are many moonlight stones. Many hunters are lost on the way, but finally they arrive. As they discover the stones, Ham Egg shoots at the trio. At the last minute, Mr. Lemonade jumps in the way and takes the bullet himself and dies. They soon discover the stones, and Ham Egg, blinded by greed, steals one of the stones and swallows it so no one else can have it, but dies shortly afterwards because the stone poisoned him. Dr. Moustache takes Leo and together they escape back down the mountain. It is then that Moustache suddenly realizes that the lion has gone blind. He rids of the stone they got because he believes it has ruined enough lives.
The film ends with Lune returning from the human's world and Dr. Moustache taking the cub to see his father's pelt. Leo died on the journey by stabbing himself with Dr. Moustache's knife. He did this so Dr. Moustache could eat his flesh and clothe himself with Leo's fur so he can tell the humans what they need to know. Lune then begins nuzzling his fur. Dr. Moustache tells Lune about what his father did, "Your father was as wise as he was brave, and you should know what he did to save the world. He was the most courageous soul I've ever met, a true king who gave his life to save the land". Then both of them head out into a meadow and see clouds in the shape of Leo.