The Empire had dispatched a series of probe ships across the galaxy to track down the Rebel's base of operations. One of them arrived on Atollon, and after it landed some kind of protocol droid emerged from it. It took a few moments to scan its surroundings and then headed out, just as it came under attack by two Krykna Spiders.
Meanwhile at Chopper Base, The Ghost Crew and Phoenix Squadron were heading out for a training exercise, leaving Zeb in charge of the whole base. However, Zeb was not happy about being left behind. He did not want to get bored or be in the company of Chopper or AP-5. AP-5 was also not so keen about Zeb being left in charge of the base, as he always assumed him to be somewhat of a "grunt". After a brief, but insulting, conversation, AP-5 went off to conduct a thorough inventory of the base's munition supplies. He offered either Zeb or Chopper to assist him but both of them past and left. The two of them arrived at the command center, where they received reports about meteors impacting on the surface nearby. The Rebel officer making this report suspected that one of them may have knocked out one of the perimeter sensors. He offered to send a unit but Zeb chose to handle this personally.
Accompanied by Chopper, only because he did not want to help AP-5 with his supply inventory, Zeb arrived at the knocked out perimeter sensor in a speeder. They had brought along a new one to take its place. As they inspected the damage, they found no evidence of a meteor crash but they did find two dead spiders and underneath the droid that was dispatched from the Empire, powerless. Zeb suggested they take it back to base and find out where it came from, but Chopper disagreed and insisted they trash it. Zeb did not listen and carried the droid back to the speeder. Word about the droid being out of contact with the Empire was soon reported back to an Imperial fleet, operated by Agent Kallus. The reporting office suggested alerting command to investigate, but Kallus recommended they be patient for now rather than waste time chasing down every temporal comm failure. Back at Chopper Base, Zeb and Chopper presented the droid to AP-5 who was still conducting his supply inventory. AP-5 identified the droid to be a protocol type, and after giving it some power to restart its systems the droid reactivated. Zeb tried to talk to it but the droid did not appear to understand due to having a damaged memory system. Then, to their surprise, the droid scanned the entire supply inventory. Both Zeb and AP-5 were impressed that they decided to keep him, making him as AP-5's assistant. Leaving the droid in Chopper and AP-5's care, Zeb was needed at the commander center for a priority message from "Fulcrum". Upon arriving, the Zeb was patched through to "Fulcrum", who warned him about a series infiltration droids being dispatched by the Empire to sweep the outer rim worlds for Rebel bases. Displaying the schematics, the droid was shown to be heavily armored and extremely dangerous. Fulcrum also revealed that they could impersonate as a harmless protocol droid, specially like the one Zeb just found. Then before signing off, Fulcrum reported that one failed to report in, and advised Zeb that if the droid remained out of contact the Empire would come after it, jeopardizing the whereabouts of their base.
Meanwhile, AP-5 and Chopper were Showing the droid around, when Zeb showed up armed with his Bo-Rile. He warned them to step away from the droid, just as it started to remember its programming and deployed its true form. Zeb opened fire and the droid attacked. The droid was revealed to be, as Fulcrum warned, well armored and very tough. Chopper tried to take it out with his shocker to no effect. However, Zeb managed to damage it and it retreated, leaking fluids. Knowing what might happen if the droid reported back to the Empire, Zeb, Chopper and AP-5 went after it by following its trail of leaking fluids. The trail eventually ended where they found a dead Astromech Droid with its power core completely drained and several key components removed. Zeb suspected that the infiltrator droid was trying to repair itself. Chopper was unable to track it and AP-5 suspects that it was still looking for more droids to consume, since the power from the Astromech they found was not enough for its needs. This gave Zeb an idea, and instructed Chopper to get its attention and lure it back to him so he could blast it. However, AP-5 pointed they were in an area housing high explosive munitions, and was not the best place to be firing blasters. So Zeb changed his plan to grabbing it so they could shut it down. With everyone in agreement, Chopper headed out to find the droid. It did not take him long to find it consuming the power of another droid. He got its attention and ran off with droid chasing after him. Then out of nowhere, Zeb jumped onto the droid and struggled to restrain it. The droid was again proven to be tough to beat. During a physical confrontation, the droid easily out muscled Zeb. However, Zeb managed to restrain it long enough for AP-5 to shut it down. Then just when they thought their problems were over, they discovered that upon deactivating the droid it had activated its fail safe and was set to self destruct which would vaporize the entire base.
The droid had already started its countdown, set to go off in twenty seconds. However, Chopper managed to temporally freeze the countdown circuit. It gave them the time they needed to move the droid to a safer location before it detonated. However, they could not just dump it because Zeb knew from Fulcrum that if the droid did not report back the Empire would come looking for it. They also could not allow it to go back, not while it was carrying information on their base. Whipping its memory was not an option and neither was disarming the warhead built into it. The droid was going to explode, and it was just a matter of when. Finally, Zeb had an idea. He suggested they could send it back to the Empire, but with some adjustments that would make the warhead go off when the droid reconnected with the Imperial network. Zeb's plan was to send the droid back to its base and explode before it uploaded its data, also taking along with it the other droids leaving the Empire with no clue of which one it was. AP-5 is stunned and found that a good idea. He made the necessary adjustments, and before reactivating it set it to return to its disarmed state. He also initiated its return to base protocol. AP-5 restarted its main system, and then everyone took cover as the droid reactivated. As AP-5 predicted, the droid returned to its protocol state and peacefully headed back to its ship. Zeb, Chopper and AP-5 followed it, just to make sure it did leave. They saw the droid arriving back at its ship, and before it could contact the Empire Zeb took out the transmitter. Following its programming, the droid powered up the engines of its ship and flew back to base.
All the droids made it back to the Imperial fleet, including the one that probed Atollon. The technicians inspected the droid that was sent to Atollon, but as a result it reset its warhead and exploded, taking all the other droids and an Imperial Star Destroyer with it. Meanwhile, the Ghost crew returned to Chopper Base just in time to hear Fulcrum congratulate the Rebels on dealing with the droid that infiltrated their base, much to the confusion of Ezra, Kanan, Hera and Sabine. Although they managed to protect the location of their base, but in doing so they had narrowed Thrawn's search to ninety-four possible locations surveyed by the infiltrator droids.
- Taylor Gray as Ezra Bridger
- Freddie Prinze, Jr. as Kanan Jarrus
- Vanessa Marshall as Hera Syndulla
- Tiya Sircar as Sabine Wren
- Steven Blum as Garazeb Orrelios / Droid Technician #1
- Stephen Stanton as AP-5 / Droid Technician #2 / Imperial Officer
- David Acord as Imperial Infiltrator Droid EXD-9 / Rebel Officer #1 / Rebel Officer #2
- David Oyelowo as Alexsandr Kallus
- Lars Mikkelsen as Thrawn
- In the original story, "Warhead" was a smaller B-story that would be occurring while the events of "Trials of the Darksaber" formed the A-story. The story was also going to be focused on Zeb and Rex, rather than teaming Zeb up with AP-5 and Chopper.
- The supply depot of Chopper Base is located on a coral leaf below the main operations leaf - the layout of the base is spread across such natural structures.
- The beginning of the episode is a reference to the beginning of The Empire Strikes Back, where a Star Destroyer deploys Viper Probe Droids down on Hoth to look for Rebels.
- Hobbie and Wedge are now dressed in Rebel Pilot uniforms.
- The explosive countdown displays in the Infiltration Droid's body is a nod to a similar device used by the alien hunter in the movie Predator.
- The image from EXD-9's point of view is layered with read-out text that includes the production number (W0LF314).