Following the Battle of Hoth, the Force-sensitive Rowan Freemaker and his family became involved in a quest to find the pieces of the Kyber Saber. Their quest brought them in conflict with the Sith agent Naare and the Hutt crime lord Graballa. Having already obtained the first three crystals with the unwitting help of Rowan, Naare stole the fourth and fifth crystals from the boy on Takodana and Ningoth. She used the B1-series battle droid Roger's transmission pack as a means of tracking them down.
In order to prevent Naare from reforging the Kyber Saber, the Freemakers traveled to Naboo, which was home to the sixth Kyber Saber crystal. After landing in the capital Theed, the Freemakers soon discovered that the crystal was hidden inside the former Theed Royal Palace, which had been revamped as the Emperor Palpatine Museum. The Museum was guarded by a contingent of stormtroopers led by the Imperial officers General Durpin and Commander Plumestriker, who regarded Naboo as a comfortable, plush posting.
The Freemakers decided to infiltrate the Emperor Palpatine Museum at night in order to find and steal the sixth Kyber Saber crystal. As part of the plan, Zander disguised himself as a maintenance crew and delivered Roger, who was disguised as a Clone Wars exhibit, inside the museum. That night, Roger broke out of his case and let the Freemakers inside the Museum. The Freemakers soon became distracted. Roger was distracted by an exhibit of his fellow B1 battle droids, R0-HK.
Zander soon got distracted by an N-1 starfighter hanging from the ceiling. Kordi was mesmerized by the sight of the regal gown worn by the late Queen Padmé Amidala. Despite being briefly distracted by a motorize pogostick, Rowan resolved to continue his mission and soon stumbled into several giant statues of Emperor Palpatine at various stages of his life. He was startled by a talking statue of the Emperor and triggered a chain reaction which knocked Zander and the N-1 fighter into the Theed Hangar.
This noise aroused Durpin and Plumestriker, who went to investigate with their stormtroopers. They found Kordi, Zander, and Roger in the Theed Hangar. After Plumestrike recognized the intruders from an earlier encounter on Kashyyyk, Durpin ordered their execution. However, Rowan had disguised himself as the Emperor, claimed that the Freemakers were wealthy donors and demoted Durpin and Plumestriker. After the guards had left, the Freemakers found the sixth Kyber Saber crystal in Kordi's royal gown.
Before the Freemakers could leave, they were stopped by Naare and the bounty hunter Dengar. A gun battle soon ensued between a blaster-armed Roger and Dengar. Meanwhile, Rowan fought Naare in a lightsaber duel. However, Naare was more powerful than him and stole the sixth Kyber Saber crystal form him. She then hurled him against the N-1 starfighter. She then retrieved her stolen Sith lightsaber. Meanwhile, Dengar accidentally destroyed R0-HK and was pursued by a vengeful Roger.
Naare then prepared to kill Rowan but the boy used the Force to release the bolt holding the N-1 fighter. The starfighter crashed and this caused the ship to release its bombs, creating and explosion which destroyed the other starships and demolished much of the Museum. The Freemakers then fled the Museum, leaving the sixth crystal in the hands of Naare.
Despite retrieving the sixth Kyber Saber crystal, Naare's actions also led to the destruction of the Emperor Palpatine Museum. As a result of the debacle, General Durpin and Plumestriker were demoted and reassign to Hoth as punishment. Meanwhile, Rowan and his siblings discovered that Naare had been spying on them using Roger's transmission pack. Both the Freemakers and Naare discovered that the seventh Kyber Saber crystal was on Hoth. In an attempt to prevent Naare from recovering the seventh crystal since she was unable to find it without Rowan, the Freemakers traveled to Zoh to seek out the help of the Maker of Zoh.
The Mission to Naboo first appeared in the LEGO Star Wars: The Freemaker Adventures episode "The Kyber Saber Crystal Chase," which first premiered on Disney XD on August 1, 2016.