In the wake of the near-destruction of the rebel fleet during many battles, the early rebellion against the Empire faced a shortage of bases for their forces. In 3 BBY, the rebels finally found Atollon by cross-referencing rebel data with the Imperial network, provided by AP-5 and the astromech droid Chopper, and successfully established the Chopper Base. After the sudden disappearance of rebel Lieutenant Dicer, they found out that one of the planet's native creatures was the Krykna, a giant spider-like predator.Eventually, they managed to ensure the base's protection using the sensor markers as a fence. Later, the former Jedi Ahsoka Tano traveled to Atollon to meet up with the Jedi Knight Kanan Jarrus, Padawan Ezra Bridger, and Chopper for a mission to Malachor.
After returning from their mission to Malachor, the blinded Kanan along with Ezra and Chopper were greeted by their fellow rebels, Rex, AP-5, and Commander Jun Sato. In 2 BBY, Atollon continued to host Chopper Base. While Kanan stayed behind to meditate in the Force, Ezra assumed a greater leadership role among Hera Syndulla's rebel cell and led a successful mission to rescue Hondo Ohnaka, a Weequay pirate who supplied the Phoenix rebel cell with information about the Imperial starfighter reclamation plant Reklam Station. While Ezra led a recon mission there, Kanan encountered Bendu, who taught him to overcome his fear of the Krykna and repair his connection to the Force. Kanan also left the Sith holocron that Ezra had obtained on Malachor in Bendu's care.
After the former Sith Maul kidnapped Hera and the other Ghost crew, Kanan and Ezra traveled on a speeder bike into Atollon's wilderness to find Bendu and retrieve the Sith holocron. There, they told Bendu that Maul planned to combine the Sith holocron with Kanan's Jedi holocron. The Bendu counselled Ezra and Kanan that doing so would provide clarity but could lead to chaos. Nevertheless, he allowed Ezra to retrieve the Sith holocron from an underground cave full of Krykna. With the help of Kanan, Ezra overcame his fear of the giant spiders and together the two retrieved the holocron.
Later, the Spectres, Rex, and Commander Sato attended a briefing at Chopper Base to discuss a mission to rescue several cadets from the Imperial Skystrike Academy who wanted to defect. The Mandalorian weapons expert Sabine Wren was assigned the mission. After rescuing the cadets, Sabine along with Wedge Antilles and Derek Klivian arrived at Chopper Base where they welcomed by Commander Sato.
After evacuating rebel dissidents and the rebel cell Iron Squadron from the planet Mykapo, Commander Sato had an emotional reunion with his nephew Mart Mattin at Chopper Base. Later, Hera, Sabine, Zeb, and Commander Sato remained at Chopper Base while Ezra, Kanan, and Chopper undertook a mission to infiltrate the Imperial Armory Complex on Lothal with Ryder Azadi's rebel cell. Ezra's team and Ryder corresponded via hologram throughout the mission. As a result of the mission, the Phoenix rebels learned that Grand Admiral Thrawn was developing a new starfighter initiative and that the Imperial Security Bureau Agent Kallus had become a rebel informant.
Using the information obtained by Ezra and Chopper, Hera began preparations for a strike on the Lothal Imperial factory. Before they could proceed with the mission, Ezra succumbed to a dark side attack by Maul. While Hera and the rest of Phoenix Squadron left for Lothal, Ezra, Kanan, and Sabine stayed behind to deal with Maul. Ezra and Kanan encountered Maul in the wilderness after communing with Bendu. Ezra agreed to follow Maul to the planet Dathomir after Maul threatened to activate a homing beacon that would alert the Empire to Chopper Base.