- King Julien
- Mountain Lemurs (antagonists)
- Koto (antagonist)
- Crocodile Ambassador
- Mountain Lemur Captain (antagonist)
- King Joey
- Zora (antagonist)
In the kingdom, Julien is telling Maurice that his "adopt an aye aye" program has given the displaced aye ayes homes in the kingdom. He tells him that the random band of mountain lemurs hasn't attacked in awhile, and that everything can go back to normal. The crocodile ambassador suddenly appears, with the other crocodiles, screaming for sanctuary.
In the plane, the Crocodile Ambassador is trying to explain to Julien what happened, but Julien can't understand his panicked mumbling. Gregor, his assistant explains that the mountain lemurs attacked their kingdom, forcing them to flee. Julien assures the crocodile ambassador that they will be safe in his kingdom for the time being. Julien tells Maurice that he's sure the mountain lemurs won't attack anyone else. However, Clover comes in to report that the mountain lemurs attacked the Rat Kingdom. Maurice is worried that the mountain lemurs will attack them too. Julien orders Maurice to gather the kingdom for an announcement.
Julien addresses his subjects, telling them that the mountain lemurs will most likely attack the kingdom. This causes a panic, but Julien stops this by assuring them he has a plan.
Overnight, the lemurs build a wall around the kingdom. Julien assures Maurice that everything can go back to normal. On the other side of the wall, Koto appears, calling for King Julien, and asking to be let in. Clover excitedly thinks he's here because of her, and calls out to him. Maurice, however, is unsure if they should let him in. Julien dismiss him and lets Koto in. Julien asks if he is on the run from the mountain lemurs, and assures Koto he's safe from them here. He shows Koto the wall, which only has one way in or out. Koto grabs the door and breaks it, opening the gate. Julien shouts at him for doing this, as Koto howls, calling mountain lemurs in through the gate. Julien quickly realizes it's Koto's that's been attacking everyone, and Koto explains he wasted his kingdom's money on his military, so he had no choice but to conquest. Koto tells Julien not to fight back, as he cannot win. Julien puts his faith in Clover to save the kingdom, but his disheartened to find her tied up by two men struggling to contain her. Mort tries to fight for King Julien, but gets stopped. Julien surrenders, telling Koto he can have the kingdom, as long as he lets his people go. Koto, not buying this, says he'll take the kingdom and he'll keep the citizens as slaves. Julien is left with one choice, and yells at everyone to run away. The people start to run away in a panic as Koto orders for their capture. Julien grabs Mort and throws him to Pancho, who is standing by the gate, but the two get knocked down. Julien yells that his people need to run away, not in circles. Clover, still bound, tells Koto he won't get away with this. Koto tells her he admires her, and will make her his queen. Clover angrily pulls away, telling him this will never happen. As she is pulled away, Clover breaks free of her binds and tries to attack Koto. However, she is scooped up by Sage and his hawk, and carried away. Clover watches as Julien and Maurice are surrounded.
In the kingdom, the citizens of the kingdoms are put in a prison camp. Mort, in the camp, tries to seduce the guard at the entrance, but she just sneezes and walks away.
At the Baobab Tree, Julien and Maurice are hanging in a cage. Julien thinks he and Koto are still friends and asks Koto to let him out. Koto refuses, and tells Julien that he needs to accept the fact that the line of Julien kings is over. Julien, hearing this, is hurt on the inside.
Julien and Maurice are brought to Koto, with Maurice asking Julien if he has a plan, to which Julien replies that he doesn't. As a tradition, Koto allows Julien to have one last request. Julien requests a dance off, and if he wins, Koto will lets his people be free and Julien will sacrifice himself willingly, and if loses, he and his people die. Koto accepts this and the dance off begins. Julien does well at first, but gets exhausted and succumbs to Koto. Koto states that dancing is part of his training. Koto announces that King Julien and Maurice will be fed to a giant snake at dawn.
Sage drops Clover on a mountain. Angrily, she asks Sage why he took her away. Sage explains she was outnumbered, as a grain of sand cannot push a wave back into the sea. Clover understands this, but is still mad at him for not letting her do her job. She tries to leave, but Sage asks where Clover is going. Clover responds she has go back to help King Julien, and tells Sage not to get in her way.
That night at the prison camp, Mort is the only one that thinks they can still help King Julien. He suggests to the others that if they work together, they can get out and help. However, but the others have already come to face that they will likely die. Mort, angered, says if they won't help, he'll save King Julien himself, and starts tunneling a hole through the ground.
Both tied to a tree, Julien says to Maurice that it is his fault that Koto got in, seeking Maurice to shoulder the blame. However, he then apologizes to him. Maurice says he's sorry too, and despite the fact they are about to die, he's proud of the king Julien has become. Julien smiles, before saying those words are useless.
At the dawn of the execution, the snake is smashing on the door, while at the prison camp, Ted is watching from on top of a crocodile. Koto's men release the snake, which frightens Julien, Maurice, and the prisoners. Julien and Maurice say their final goodbyes to each other. The snake charges at them, but before he can eat them, Mort comes up from the ground. Mort seduces the snake. Koto's men offer to get him, but Koto says he'll be eaten soon enough. Mort teases the snake, hypnotizing him, but when Mort puts his hand on his eye, the hypnosis stops and he chases after him. Julien yells at Mort to stop playing around and untie him and Maurice.
The crocodile complements Mort's bravery, and the others say they will die anyway, so they should fight too. Hector tells everyone to bust down the door, and the crocodile charges through, knocking down two guards. Koto notices the prisoners charging and orders his men to get them. The mountain lemurs charge at them which causes the prisoners the panic. The prisoners put up a good fight, with the Crocodile Ambassador and his crocodiles holding off some mountain lemurs, and King Joey commanding his rats to launch the aye ayes as stink bombs into the midst. Julien slips out of his restraints, and he and Maurice run away. The snake loses his attention on Mort and goes after Julien. The snake hits Julien with his tail, which knocks Julien's crown off and Julien lands on Pancho. Julien tries to go after his crown, but Pancho stops him. Pancho says they can get to the submarine and get out of here, but Julien doesn't want to leave his people. Maurice grabs Julien's arm and takes him away far to the woods and says they can't take on the mountain lemurs, so they have to get out of there to get help and make a plan. Julien looks on as his people are being forced back into the camp.
Julien runs away as Koto steps on his crown, looking for him. Mort yells at King Julien to run, saying he'll be okay, before being tossed around by the snake. Julien looks at Mort screaming. Julien raises his hand to Mort and sadly says goodbye to him. Julien and Maurice enter the submarine and Maurice tells Pancho to launch it. Pancho then punches the button and the submarine takes them away.
Clover runs back to the kingdom to join the fight, but sees the prisoners being put back in the camp. She sees that King Julien is not in the cage, and goes to the plane. She looks in the plane to see Koto walking into the throne room. One of Koto's men repots that the prisoners are back in the camp, but King Julien escaped. He offers to dispatch a search party to go after him, but Koto says to forget him, since soon King Julien will be nothing more than a forgotten memory. Mort is forced into the throne room, carrying Julien's crown. Koto takes the crown and sits on Julien's throne.
Sage plops next to Clover as she buries her face in her paws. She says to herself that this is her fault, despite it being Julien's, and that she must make this right. She must free the prisoners, and make Koto pay. Sage says that she can't do it alone, and Clover admits that he's right, asking for his help. Sage nods in agreement.
Mort is thrown back into the camp. Willie holds him as Mort sobs. The others in the background glare at Mort in pity and glare in horror at the ruthlessness of the mountain lemurs.
Julien and Maurice look back at the kingdom, saddened. Heartbroken, Julien laments in sadness by the loss of his kingdom. Maurice comforts him and says to Julien that they'll find a way to get his kingdom back. They glare at the kingdom one last time for a few moments, until Maurice despodently closes the door as he and Julien re-enter the submarine as it dives into the ocean.