Chopper Base was built on the Atollon Coral Mesa, a broad flat-topped elevation covered in huge coralline formations in 3 BBY with the salvaged and looted parts of the Imperial Class four container transport, Cargo transport 241. The northern perimeter was near a nest inhabited by krykna, large spidery creatures that devoured sentient beings. To ward off the krykna, a perimeter fence consisting of sensor beacons was constructed in the northern perimeter. The base hosted runways for landing ships and a command center that was equipped with holograms for receiving and sending offworld transmissions. The base also held a supply depot that had their rations, explosives, and cargo. Most of the base's inhabitants appeared to reside in rebel ships like the Spectres' VCX-100 light freighter Ghost.
In 3 BBY, the Phoenix Cell discovered the uncharted planet of Atollon after receiving coordinates for a safe world from AP-5, a former Imperial inventory droid that the rebel astromech droid Chopper had befriended. To honor Chopper for his part in discovering Atollon, the base was named Chopper Base. After the Krykna devoured Lieutenant Dicer and attacked the Spectres and Captain Rex, the rebels constructed a fence consisting of sensor markers around Chopper Base's northern perimeter. Rex was placed in charge of overseeing the base's operations.
The former Jedi Ahsoka Tano rendezvoused with Kanan Jarrus, his apprentice Ezra Bridger, and Chopper for a mission to Malachor. Ahsoka was lost during the mission, but Kanan, Ezra, and Chopper managed to return to Chopper base in the shuttle Phantom. There, they were received by Hera, the other crew of the Ghost, Rex, AP-5, and the Phoenix Cell's Commander Jun Sato.
A year later, Chopper Base's command center hosted a visitor in the form of Hondo Ohnaka, a Weequay pirate whom Ezra had rescued from the Imperial prison on Naraka. During the briefing, Hondo informed the Spectres, Rex, and Commander Sato about an Imperial starship reclamation plant called Reklam Station in return for the rebels giving him a starship after the recon mission. After Ezra's recon mission went away, Kanan, Hera and the rest of Phoenix Squadron departed to rescue Ezra and his team.
Later, the Spectres and Commander Sato attended a briefing at Chopper Base's command center where the rebels received a transmission from a Fulcrum informant that several cadets from the Imperial Skystrike Academy were wanting to defect. The Mandalorian weapons expert Sabine Wren was placed in charge of the mission. After escaping with the cadets Wedge Antilles and Derek Klivian, Sabine and the cadets were greeted by Commander Sato at Chopper Base's runway. He personally welcomed Wedge and Derek into the Rebellion.
During a recon mission to the third moon of Concord Dawn, Sabine and her former adversary Fenn Rau worked together to prevent Gar Saxon, the leader of the Imperial Super Commandos from taking the shuttle Phantom II and discovering the location of Chopper Base. Following a successful mission to evacuate rebel sympathizers on Mykapo, Commander Sato had an emotional reunion with his nephew Mart Mattin, the leader of the Iron Squadron, on Chopper Base's runway.
During Ezra's undercover mission at the Lothal Imperial Armory Complex, Hera, Sabine, Zeb, and Commander Sato corresponded with Ezra, Kanan, and the Lothalian rebel leader Ryder Azadi via hologram from the safety of the Chopper Base command center. As a result of Ezra and his team's mission, the Phoenix Squadron learned that Grand Admiral Thrawn was developing a new starfighter initiative and that the Imperial Security Bureau Agent Kallus had become a Fulcrum operative.
Using Ezra and his team's information, Hera began planning a strike on the Lothal Imperial factory. During a briefing at the Chopper Base command room, Ezra began experiencing dark side visions of the former Sith Maul, whom he had previously encountered at Vizsla Keep 09. Despite insisting that he was fit, Hera was forced to relieve Ezra of his duties after the young Jedi almost killed a rebel trooper, whom he had mistaken for Maul. At the advice of Kanan, Hera, and the other rebels proceeded with the mission while Ezra, Kanan, and Sabine stayed behind to confront Maul.
Ezra agreed to follow Maul to the planet Dathomir after the latter threatened to activate a homing beacon that would alert the Empire to Chopper Base should he die. Sabine managed to track Ezra using a tracker she had planted on his wrist comm. Kanan and Sabine followed Ezra on the shuttle Phantom II.
Later, most of the Phoenix rebels and Spectres departed for a training exercise. Captain Zeb, Chopper, AP-5, a communications officer, and some Rebel troops stayed behind to guard the base. During that time, an E-XD-series infiltrator droid designated EXD-9 discovered the base but was knocked out by two krykna. Later, Zeb and Chopper found him and brought him back to the base to be repaired. After repairing him, AP-5 set EXD-9 to work as an assistant inventory droid. After receiving a warning from Fulcrum about the Infiltrator Droid, Zeb along with Chopper and AP-5 joined forces to overpower EXD-9 before he could alert the Empire. After reprogramming him, they sent him back as a rigged bomb to the Empire. EXD-9 destroyed an Imperial Star Destroyer and managed to delay the Empire's efforts to locate Chopper Base.
After Sabine reluctantly agreed to learn how to wield the Darksaber in order to lead the Mandalorian people, Kanan and Ezra took her to the wilderness to begin her training. Kanan regarded Chopper Base as providing too many unnecessary distractions. Hera stayed behind at Chopper Base and corresponded with Kanan via hologram. Later, Fenn Rau departed Chopper Base on a speeder bike to ferry the other rebels supplies.
Chopper Base's location was almost exposed on two occasions. With the help of the rogue Imperial Security Bureau Agent Kallus, Chopper managed to delete the base's location from Thrawn's star chart. Later, a team of Imperial slicers reprogrammed Chopper with the intention of finding the location of Chopper Base. Their plot was foiled by Hera and the Spectres following a mission to Killun Station. The former Imperial Senator Mon Mothma's speech announcing the formation of the Alliance to Restore the Republic was witnessed by several Phoenix rebels including Commander Sato, Rex, and AP-5 at Chopper Base.
After receiving messages from Kanan's Jedi holocron and the Sith holocron from Malachor indicating that Master Kenobi was in danger, Ezra and Chopper managed to sneak off Chopper Base in a stolen RZ-1T trainer. Hera had forbade Ezra from leaving since she needed him to train for the upcoming attack on Lothal. They later returned to Chopper Base after Kenobi defeated Maul in combat and sent them back to help the Rebellion. Despite the rebels' efforts to keep the base hidden, Thrawn discovered Chopper Base and send his Seventh Fleet to attack the Atollon system. Thrawn's forces inflicted heavy casualties on the Phoenix Squadron and General Jan Dodonna's Massassi Group, which had been massing for an attack on the Imperial TIE Defender factories on Lothal. Chopper Base was also destroyed by Imperial bombardment and the Bendu, who summoned a storm that terrorized both sides.