Whenever the Republic clone army got defeated in battle against the Separatists, what happened
to the clones that were captured and taken prisoner?
Well the capture of clones after battle varied depending on the Separatist commander and
general, as there were many instances where the battle droids were programmed to not take
any prisoners and just continued to kill the clones, regardless of their surrender.
When a capture order was given however, the clones were taken prisoner usually for two
reasons: for interrogation or to be used as an asset for negotiation.
Typically high ranking clones and those that specialised in datawork and intelligence were
taken for interrogation, as they tended to know the movement of nearby Republic forces
or the whereabouts of fleets and outposts.
Interrogations more than often involved torture, both physical and psychological.
A good example of this was with Arc Trooper Alpha, who was captured by Ventress.
The bound trooper was beaten, cut up with a knife, and perhaps even shocked by the darksider,
all the while she demanded the whereabouts of Republic medical facilities.
The trooper persisted in remaining silent, telling her that he wasn’t trained to answer
questions and only to fight, with the only information he gave her was his identification
number and the general he served.
Ventress also tried to play mind games with him, by telling him that he was only fodder
to the Republic and trained just to die for a false purpose.
Despite this, the clone still remained silent.
Frustrated at the lack of progress in her interrogation, Ventress decided to give the
Clone some time to think about his situation and try the next day, in which if she were
to fail again she’d likely kill the clone for still refusing to reveal anything.
It’s likely most captured clones that held vital intelligence were treated similarly
by their captors, as they weren’t exactly viewed as real living beings.
Plus many Separatist commanders and generals tended not to care much about the treatment
of their enemy, whether they be soldiers or civilians.
Clones were indeed trained to resist revealing information during interrogations, and perhaps
even biologically modified to some extent with even being mentally incapable of revealing
such information.
That they’d rather die than betray their Republic.
It’s safe to say that most clones that were taken prisoner by the Separatists, likely
ended up being killed shortly afterwards.
Other clones were sometimes used as a bargaining chip or perhaps even as meat shields, as the
Jedi tended to view them more than cannon fodder and would be more willing to negotiate
their release or be reluctant to attack certain positions if they knew captured clones were
present.
These next two parts also applies to Canon.
First is clone trooper Tups, who was taken by the Separatists after executing one of
his Jedi Generals.
The Separatists found this action by him to be very intriguing, and they believed that
by capturing him they could uncover the cause and use it to develop a weapon that would
force a similar reaction among the other clones that’ll cause them to betray their own Jedi
amidst battle.
The other clone is actually Echo, who despite being blown up and believed to have been killed
by his fellow troopers, he was instead taken alive and turned into a cyborg by the Separatists.
They then experimented on his body before putting him into stasis and probing his mind
which revealed Republic strategies and attack patterns, which were then fed to Separatist
commanders during battles which allowed them to predict the tactics of the Republic.
So it seems like as the war neared the end, the Separatists were able to develop a technology
that allowed them to bypass the interrogation stage of gaining intelligence from the clones,
and instead were able to just extract it from them forcibly through a machine without the
clone even having the ability to fight it.