In the year 2 BBY, the Imperial Grand Admiral known as Thrawn initiated the deployment of E-XD-series infiltrator droids across numerous planets situated in the Outer Rim. Among these droids, one designated as EXD-9 was dispatched to Atollon, which served as the location of Chopper Base, the home of Phoenix Cell. Soon after its arrival, EXD-9 was caught in an ambush by several krykna spiders, resulting in its incapacitation. Captain Garazeb Orrelios and Chopper later discovered the damaged infiltrator droid and transported it back to their base. Mistaking EXD-9 for a simple protocol droid, they assigned it the task of assisting AP-5 in managing the inventory of the base depot. Upon discovering EXD-9's true identity as an Imperial Infiltrator droid, Zeb, Chopper, and AP-5 collaborated to subdue and deactivate it. To prevent the Empire from uncovering the location of Chopper Base, the rebels decided to send the droid back to its original Star Destroyer, but with its proton warhead primed to detonate upon reconnection to the Imperial network. EXD-9 ultimately succeeded in destroying the Star Destroyer, but this incident aided Thrawn in narrowing down his search for the rebel base to the 94 systems where the droids had been dispatched.
In the year 2 BBY, Grand Admiral Thrawn initiated a program to send out E-XD-series infiltrator droids across the Outer Rim Territories with the goal of finding rebel bases. These droids were designed with a proton warhead that would self-destruct if captured, though this was against Imperial regulations. They had two modes: a combat mode, where they were incredibly quick and agile, and a protocol mode, where they looked like ordinary protocol droids. One of these droids, known as EXD-9, was sent to the planet Atollon, the site of Phoenix Cell's Chopper Base. After landing, EXD-9 was set upon by two krykna, native spider-like creatures known for their toughness, and was temporarily put out of action.
EXD-9's arrival happened while most of the Phoenix rebels, including the majority of the Spectres, were away on a training exercise. The Lasat warrior Garazeb Orrelios was responsible for maintaining the base's security. The remaining members of the stay-behind group included the C1-series astromech droid Chopper, the RA-7 protocol droid AP-5, and a communications officer working in the command center. After the comms officer reported that a sensor beacon in Sector 6 seemed to have been damaged by meteors, Zeb and Chopper went to investigate.
Upon their arrival, Zeb and Chopper replaced the sensor beacon and then discovered EXD-9 amidst a pile of dead krykna. They mistakenly thought it was just an old protocol droid. Feeling sorry for the lost and damaged droid, Zeb brought EXD-9 back to Chopper Base. Chopper suggested destroying the droid immediately, but Zeb disagreed. Back at the base, AP-5 recharged the droid, which then began scanning the depot. Due to the damage it had sustained from the krykna attack, EXD-9 initially had no memory of its mission. AP-5, believing that EXD-9 would be useful for inventory management, hired the "protocol droid" as his assistant.
Later on, Zeb received a transmission from Fulcrum, warning that the Empire had deployed Infiltrator droids and that they had lost contact with one of them. After examining the schematics, Zeb realized that EXD-9 was actually an Infiltrator droid. Fulcrum was in fact Agent Kallus of the Imperial Security Bureau, who had become disillusioned and was aiding the rebellion by providing intelligence on Imperial activities since his encounter with Zeb on Bahryn. Kallus had recently been informed that one of the Infiltrator droids had failed to report back and, suspecting that the rebels had it, had bought time by arguing that the Empire was too busy to investigate every minor comm failure, and that they would only investigate if the droid failed to report back after a full cycle. In his transmission, he also warned that if the droid didn't report back, the Empire would come looking for it.
Zeb returned to the depot just in time to warn AP-5 and Chopper before EXD-9 switched to its attack mode. The droid had regained its memory and remembered its true mission after AP-5 used the words "rebel base." The Infiltrator droid attacked the rebels and engaged Zeb in combat. During the fight, Zeb managed to sever part of the droid's left hand. Damaged, EXD-9 retreated to recharge and repair itself. It attacked another astromech droid and a GNK-series power droid, draining their power and cannibalizing their parts to recharge and repair itself. Due to the damage it had taken earlier, EXD-9's power readings were so low that Chopper couldn't detect the infiltrator on his scanners. As a result, Zeb and the droids came up with a plan to lure EXD-9 out of hiding so they could disable it.
Chopper successfully lured EXD-9 out of hiding, and Zeb attacked the droid using the electrostaff mode of his bo-rifle. Shooting at the droid was too risky because they were in the weapons depot, surrounded by explosives. After a difficult fight, Zeb managed to pin down the Infiltrator droid long enough for AP-5 to disable it. When the droid began to activate its proton warhead, Chopper managed to freeze the timer before it could detonate. The rebels then faced a difficult decision. They knew that the Empire would search for the droid, and they also needed to keep Chopper Base a secret. AP-5 also pointed out that, because the countdown had already started, the warhead was inevitably going to explode. After some discussion, Zeb and the droids decided to reactivate EXD-9 in its disarmed mode and return the droid to its base, along with the proton warhead. AP-5 also programmed EXD-9 to explode once it reconnected to the Imperial network.
After reactivating EXD-9, Zeb, AP-5, and Chopper allowed the Infiltrator droid to walk back to its pod. Following EXD-9, Zeb shot out the pod's long-range transmitter. This forced EXD-9 to take its pod back to the Imperial Star Destroyer it had launched from. Upon arrival, two Imperial Navy technicians reconnected EXD-9 to the Imperial network. This caused the Infiltrator droid to begin its proton warhead countdown and detonate, which also destroyed the other Infiltrator droids. The resulting chain reaction of powerful explosions completely destroyed the Star Destroyer. The explosion was witnessed by Agent Kallus and other Imperial officers aboard a nearby Star Destroyer. While he publicly expressed shock and anger, Kallus secretly smiled.
The next day, Zeb contacted Hera Syndulla and the other Spectres to inform her about what had happened, but assured her that they had everything under control. The Spectres later attended a briefing at Chopper Base's command center, where they received a message from Fulcrum congratulating them for reprogramming the Infiltrator droid that he had warned them about and setting it to self-destruct. AP-5 tried to tell the other Spectres the entire story, but Zeb, feeling embarrassed, stopped him.
Grand Admiral Thrawn learned about EXD-9's role in the destruction of the Star Destroyer from Kallus, and praised the rebels' clever plan. Despite this setback, Thrawn was in good spirits because he had narrowed down his search for the Phoenix rebel base to the 94 systems where the droids had been sent. He vowed to crush the rebellion once and for all.
EXD-9's infiltration of Chopper Base was the central plot point of the Star Wars Rebels episode titled "Warhead," which was first broadcast on January 14, 2017. The background and specific details of the plot were further elaborated on in a Rebels Recon video hosted by Andi Gutierrez and Pablo Hidalgo.