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In season 1 episode 6 of Star Wars: The Clone Wars, we are introduced to R3-S6, a droid meant to replace R2-D2. R2-D2 had been damaged in an earlier scene (and was presumed destroyed). In episode 7, we learn R3-S6 was a Separatist spy.

Presumably, the Republic had strict controls and security over the manufacture, delivery, and inventorying of its droids. For example, it might have had strict standards for a droid to meet. Maybe everyone involved in droid manufacturing, delivery, and/or inventorying was required to maintain a security clearance. Maybe the droids were guarded by members of the Grand Army of the Republic.

How did R3-S6 find his way onto a Republic base and, eventually, Anakin's starship without anyone even suspecting that R3-S6 was a Separatist?

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  • At the point of the Clone Wars, we see a Republic in its twilight days (minutes?). Revenge of the Sith opens with “ War! The Republic is crumbling under attacks by the ruthless Sith Lord, Count Dooku...” This is against Lucas’ backdrop of the Adventures of the Starkiller: “ The REPUBLIC GALACTICA is dead. Ruthless trader barons, driven by greed and the lust for power, have replaced enlightenment with oppression, and "rule by the people" with the FIRST GALACTIC EMPIRE...” There’s no reason to believe Republic QA-QC is high at this time. Nov 23, 2021 at 1:14

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From Star Wars: The Clone Wars: The Visual Guide:

R3's Secret

R3 is actually a spy: Separatist agents in the Republic military sabotaged his programming and arranged for him to be sent to Bothawui.

(page 100)

This is elaborated upon in Star Wars: The Clone Wars: The Official Episode Guide: Season 1:

After R2-D2 sent R3-S6 on a one-way trip to the surface of Ruusan 2, Republic Intelligence discovered that Separatist slicers working at a forward supply base on Milagro had altered Goldie's programming. A number of astromechs on Milagro got replacement domes, letting the slicers introduce "sleeper" programs directing them to secretly contact Separatist forces in the vicinity and obey their orders. (The mismatch between Goldie's R3 designation and R2-class dome didn't arouse suspicions—astromechs were often repaired with non-standard parts.)

The Milagro Incident barely made news: Throughout the Clone Wars, Separatist and Republic spies sabotaged each other's factories, supply lines, and droids.

(page 63, emphasis added)

From this, we can infer that the Republic's security wasn't strong enough to prevent sabotage, including from double agents, and that this in fact happened fairly often.

Note that these sources are technically Legends material, but as far as I know don't contradict anything in Canon.

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    This might be a good plot for a new TV episode. Heck, maybe a new series: "Star Wars Separatists"
    – moonman239
    Nov 23, 2021 at 1:38
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    When two sides in a conflict are more or less evenly matched in terms of technological and intelligence capabilities, both sides will likely have a reasonably good success rate in hostile operations, simply because this sort of game favors the attacker, who can choose where, when and how to strike, over the defender, who has to be on guard on all possible targets continuously. Nov 23, 2021 at 9:36
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Droids in Star Wars aren't really seen as rational actors, more as pieces of equipment. People are not really expected to have a personal relationship with it, like you wouldn't also expect a car's navigation device as hostile or friendly?

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  • You could improve this answer by editing it to include some supporting evidence, such as a relevant quote or quotes, like the ones in Milo P's answer. Nov 23, 2021 at 14:21

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