Julien conducts an elaborate lie, blaming a giant "mega-gecko" for ruining a young lemur's birthday party.
While walking through the jungle, King Julien comes across a party, for someone named Todd, and questions why he wasn't invited. A flashback is seen of him throwing out Todd's invitation as junk mail. Julien decides to have some of the cake before he leaves. When he tries to eat some, a fly bothers him, and Julien ends up wrecking the party trying to get the fly away. Clover, Maurice, and the rest of the lemurs show up to the party as Ted accuses Julien of hating Todd. Before jumping to a conclusion, Maurice assures the lemurs that King Julien has an explanation for the mess. Julien comes up with a lie that a "Mega Gecko" ruined the party, and explained that the gecko has red eyes, eats lemurs and cake, and is allergic to nuts. Hearing this makes the lemurs love Julien even more. During the rest of the day, the lemurs make up rumors about the Mega Gecko.
At the plane, Maurice complements that Julien's approval rating is 130 percent, and the lemurs love him more than ever. Julien gloats their reasoning is because he defeated the Mega Gecko.
That night at Maurice's hut, Maurice tries to fall asleep, but has nightmares of running away from the giant Mega Gecko.
The next morning, Julien wakes up to Masikura, who has news for him. Apparently, the lemurs are accusing random lizards of being spies for the Mega Gecko, and Dorothy has begun a nut drive for combatting the Mega Gecko. Julien says this is harmless, until he learns that all cake is a "security risk", and yells for Maurice.
In the throne room, Maurice is talking to Amelia about his nightmares. When Julien comes in, he's asking why Maurice is talking to Amelia. Maurice says he was looking for the bathroom. Julien calls him weird, then he starts to talks to Amelia about his problems. He say's the lemurs are ruining good cake and the Mega Gecko was the worst thing that never happen. Amelia nods her head, which Julien interprets as telling the truth. Julien disagrees with her advice, since the lemurs will know he lied and comments how Maurice gives better advice, which gives him an idea.
At the gathering, Julien plans to make a speech to the kingdom but makes Maurice do it. Julien tells Maurice to tell everyone that everything is fine, but Maurice starts telling the lemurs about his nightmares, which makes the lemurs panic. Julien pushes Maurice aside and tells the lemurs to ignore what he just said. Clover steps to the floors and says the only option to do now is to hunt the mega gecko, which rallies the lemurs. Julien asks Clover what she will do if she can't find the mega gecko. Clover responds with "I won't eat! I won't sleep! I'll neglect important personal relationships."
Julien goes to Timo and request him to build a giant gecko and gives him a picture. Timo has questions, but Julien says he won't answer any questions.
Back at Timo's place, Timo questions Julien why he wants him to build a giant mechanical gecko and let it loose. Julien's lies and says it's for Todd as a gift. Julien tells Timo to remove the bunny ears since his picture didn't have bunny ears. Timo activates the gecko and it walks into the woods.
At Clover's hunting party, Clover spots the mega gecko's tracks, and while they follow it, they run into Julien. Clover asks Julien who's watching over the kingdom, and Julien says he left Maurice in charge, with Maurice shown shivering in fear on the throne. Julien says to Clover that she's going the wrong way and he leads the hunting party another way, while in the background, the Mega Gecko goes the opposite way. Julien leads the group to spot where the Mecko Gecko should be, only to find out it's not there. The Mega Gecko tracks in an circle, Clover figures out that the Mega Gecko is tracking them. Willie, Ted, and Horst panic, but Clover calms them down and says that they are going to trap the gecko, and grabs Mort's cake to use as bait.
In the evening, Clover is preparing the trap, and during the night, the trap activates. But, when the group checks, they find Mort was the one who activated it. Clover decides the group will make camp for the night and orders Mort to stand guard. During Mort's watch, he gets eaten by the Mega Gecko.
In the morning, the group finds Mort missing, and Clover finds that the Mega Gecko is heading towards the kingdom. She and Julien head toward the kingdom.
At the kingdom, the Mega Gecko is screaming causing everyone to panic. Clover says she'll defeat it, but Julien steps in front, confidently, to defeat the Mega Gecko. Julien walks towards it trying to find the off switch, but gets chase away by the Mega Gecko breathing fire at him. Julien heads towards to Timo and Timo explains there are some wrongs in the Gecko programs.
In the throne room, Maurice is frozen in fear tries to give himself courage to face the Gecko. He gets off the chair and pushes himself with his tail.
Back on the ground, Ted finds a harpoon gun as a weapon, and Clover tells him to shoot the Mega Gecko, but Ted uses the gun as a club, and he gets eaten by the Mega gecko.
Julien ask Timo if there's a off switch and Timo says the off switch was on the bunny ears. Timo figures out the manual override switch on the gecko and pulls out blueprints. Clover comes over and sees the blueprints, and questions what it is. Timo explains that Julien asked him to build a Mega Gecko. Clover is rightfully angry with Julien, but Julien shifts the blame to "Todd's secret birthday". Clover asks how they turn it off. Timo explains the override switch is in the gecko's butt. Clover volunteers herself to go into the gecko to shut it down.
In the plane, Maurice is continuing to move himself with his tail.
Back on ground, Clover prepares a trampoline to launch herself into the gecko. Julien and Timo lead the Gecko, but the gecko loses sight of them and catches Clover off guard, swallowing her. Timo runs away and Julien tells him to come back. Mauirce falls on top Julien and Julien is glad cause he thought he had to do something. Julien question why he's stiff and Maurice explains he's paralyze with fear. Julien orders Maurice to get in the gecko's butt, but Maurice says he can't leaving Julien to do it. The Mega Gecko stands above the trampoline and Julien runs for it, but he gets stuck inside the gecko's butt.
Maurice, not wanting it to end this way, pushes himself towards the trampoline and jumps, to give Julien a push. Clover guides Julien to the switch, and he reaches for the override switch and shuts the gecko down. The gecko falls down a cliff, but before it lands, Julien fires the harpoon to the cliff, launching the group to safety.
At Todd's Birthday, everyone is partying and there's a sign of Julien saying sorry he lied. Julien complements Maurice bravery of overcoming his fear and getting Julien out of the gecko's butt. Maurice is just glad it is all over, but at the wreckage of the Mega Gecko, it's eye turns red.