Following the rescue of Hera Syndulla, the Spectres embarked on an operation to investigate the activities of the Galactic Empire at the Lothal Jedi Temple during 1 BBY. With the aid of loth-wolves for transportation, the Spectres discovered that Imperial Minister Veris Hydan was attempting to unlock a portal to the World Between Worlds, intending to grant Galactic Emperor Darth Sidious control over the entire universe. Ezra Bridger and Sabine Wren infiltrated the Imperial encampment. Sabine was captured, but Ezra successfully entered the World Between Worlds, where he rescued Ahsoka Tano. After a brief ordeal connected to Kanan Jarrus's death, Ezra and Ahsoka evaded the Emperor and returned to their respective timelines. Prior to their escape, Ezra and his fellow Spectres managed to close the portal, resulting in the Temple's descent into the ground.
After the passing of Kanan Jarrus, his Padawan, Ezra Bridger, encountered several loth-wolves, including a white alpha named "Dume." Kanan's will had been transferred into "Dume" after his demise. Dume informed Ezra that the Galactic Empire was engaged in a "terrible" activity at the Lothal Jedi Temple and provided him with a stone bearing symbols that corresponded to the hand positions depicted in a mural of Force wielders outside the Temple. Following consultation with his fellow Spectres, Ezra and his rebel allies resolved to undertake the mission together.
Although the Jedi Temple was situated far to the north, the Spectres managed to travel by riding loth-wolves, capable of rapid transit through hyper tunnels. Upon reaching the Lothal Jedi Temple, they observed that the Empire and the Mining Guild had established a camp outside the Temple and were in the process of excavating various objects, including paintings and artifacts. Minister Veris Hydan oversaw this Imperial excavation project, acting on orders from the Emperor to unlock a portal that led to the World Between Worlds, a realm that could potentially grant control over time and the universe.

Given the sensitive nature of the Imperial excavation, the Lothal Jedi Temple was defended by stormtroopers, scout troopers, and the elite Death troopers. While Hera Syndulla, Garazeb Orrelios, and Chopper kept watch from the perimeter, Ezra and Sabine Wren infiltrated the encampment. With Zeb's assistance, they incapacitated scout troopers LS-515 and LS-412 and appropriated their armor. Inside the camp, Ezra and Sabine began examining the artifacts, only to be confronted by Minister Hydan, who had prohibited touching any of the objects. When the commander of the death troopers insisted on verifying their numbers and clearance codes, Ezra employed a Jedi mind trick to dissuade him.
With Chopper's assistance, the Spectres also intercepted a HoloNet conversation between the Emperor and Minister Hydan. Hydan informed the Emperor that his excavation team had reached the temple's foundations and uncovered a mural resembling the art from the former Jedi Temple relating to the Force wielders of Mortis: the Father, Daughter, and the Son. The Emperor tasked Hydan with unlocking the temple to access the conduit between the living and the dead. Despite Hera's desire to withdraw the team, Ezra insisted on continuing the mission. Ultimately, Hera permitted Ezra and Sabine to proceed, but cautioned them to be ready to abort the mission.
As Minister Hydan ordered the deployment of a Mining Guild excavation driller into position, Ezra and Sabine became intrigued by the mural of the Force wielders. Examining a hologram image of the stone, Sabine realized that the symbols on the stone corresponded to the hand positions of the Daughter, Father, and Son. While Sabine kept watch, Ezra studied the mural, seeking a way to unlock the portal. Sabine was spotted by a pair of stormtroopers, who noted that she was outside a designated patrol area. They brought her to Minister Hydan, who quickly identified her as a rebel infiltrator.

Despite Sabine's capture, Ezra continued his mission. He successfully unlocked the portal by touching the Daughter's hand, which triggered a chain reaction, causing the loth-wolves in the mural to "walk" to the right. Ezra followed the loth-wolves, which formed a circular portal. Minister Hydan and several Imperial troops soon cornered Ezra, but the rebel managed to escape through the Gateway. Stormtroopers attempted to follow, but the Gateway sealed behind him, leaving them on the other side. Minister Hydan then focused on interrogating Sabine to discover how to unlock the portal.
After entering the portal, Ezra found himself within the World Between Worlds, a mystical realm connecting all space and time. Ezra also heard the voices of various individuals from the past, present, and future, including Jedi Masters Obi-Wan Kenobi, Yoda, and Darth Vader. Meanwhile, Minister Hydan attempted to gain Sabine's cooperation in unlocking the portal through flattery, showing particular interest in the altered hand and head positions of the Force wielders on the mural. When she refused to cooperate and taunted him, Hydan instructed one of his Death troopers to strike her head with the butt of his blaster rifle.
Meanwhile, Hera, Zeb, and Chopper continued monitoring the situation, despite losing contact with both Sabine and Ezra. At Hera's urging, the Spectres infiltrated the camp to free Sabine. Hera decided to activate one of the thrusters beneath Hydan's mobile command center to create a diversion for Sabine's rescue. Hera also tasked Zeb with discreetly signaling Sabine when the thruster was ready. Chopper maintained watch over the excavation site.
Inside the World Between Worlds, Ezra encountered the convor Morai, a winged bird associated with his old friend Ahsoka Tano. He then came across a portal showing Tano dueling Darth Vader at the Malachor Sith Temple during their fateful mission to Malachor two years prior. As they fought, Tano's lightsaber struck the Malachor superweapon, causing the floor to collapse beneath them. Before Tano could fall into the chasm, Ezra pulled her to safety.

Upon awakening, Ezra reunited with Tano, who expressed her gratitude to him and Morai for saving her. When Tano inquired about how he arrived and Kanan's whereabouts, Ezra revealed that two years had passed since their last encounter on Malachor. After Ezra recounted Kanan's last stand and death, Tano revealed that Kanan had become one with the Cosmic Force and that his presence had transferred into the loth-wolf known as "Dume." Believing he could save his late master as he had saved Tano, Ezra approached a portal showing Kanan holding back the fiery explosion during their escape from the Lothal City fuel depot.
Realizing that Kanan's sacrifice had enabled the other rebels to escape, Tano convinced the younger Jedi to honor his master's sacrifice, as Kanan had found his calling in life. Ezra agreed and understood that this was his master's final lesson. After hearing rumbling sounds, Tano told Ezra they had to seal the portal and return to their own times. Before they could, the Emperor appeared on the other side of the portal, attempting to use Sith sorcery to capture Ezra and Ahsoka, two enemies who had evaded the Empire.
Back at Hydan's mobile command center, Sabine realized that the Son was the key to sealing the portal. When Hydan suggested they could collaborate, Sabine received a coded signal in the form of knocking from Zeb. Meanwhile, Hera activated the thruster, causing the mobile command center to tilt and fall onto its top. Sabine and her rebel comrades managed to escape the collapsing command center before it crashed onto several crates in the landing pad. They then headed towards the portal to rescue Ezra.

Meanwhile, Ezra and Ahsoka fled from the Emperor's blue flames, which manifested as tendrils. One of the tendrils ensnared Ezra's ankle, but Ahsoka severed it with her lightsabers. The two then managed to return to their portals, thwarting the Emperor's attempts to capture them. Ezra emerged from the portal just as his fellow rebels arrived. They were pursued by Imperial troops, but Chopper hijacked the Mining Guild excavation driller and forced the Imperials to retreat from the portal.
At Ezra's urging, the rebels worked together to seal the portal. Guided by Sabine and with Zeb's assistance, Ezra touched the Son, who hinted at the possibility of altering the future. Ezra stumbled back onto Zeb, who caught him. The Father then moved his hand as the Son joined his hands and sunk with the Daughter. The rebels then escaped aboard the excavation drill as the Lothal Jedi Temple sank into the ground, consuming Hydan in the process.
Following their escape from the Lothal Jedi Temple, Sabine drove them to safety while Ezra experienced a Force vision from Kanan, who assured him that the Force would always be with him. Later, they journeyed to the site where Ezra and Kanan had first entered the Temple for his Jedi Trials four years earlier. Ezra and Hera then came to terms with Kanan's passing before returning to the driller. The sealing of the portal to the World between Worlds and the sinking of the Jedi Temple thwarted the Emperor's ambition to manipulate time in his quest for universal domination.
The Mission to the Lothal Jedi Temple was initially featured in the Star Wars Rebels Season Four episodes "Wolves and a Door" and "A World Between Worlds," which premiered on Disney XD on February 26, 2018.