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In Season 6 Episode 2 "Conspiracy" of Star Wars: The Clone Wars, as

clone trooper "Tup" is dying,

he states that "the mission" and "the nightmares" are gone.

Similarly, in Season 6 Episode 3 "Fugitive" as

clone trooper "Fives" is dying,

he states that the "mission" and "nightmares" are gone.

What are they talking about?

The only unique circumstances connecting these troopers that I can think of is that neither of them

had the Order 66 bio chip in their heads when they died.

That leads me to speculate that both the "mission" and the "nightmares" are related to it, though that doesn't give me any clues of what the "mission" and "nightmares" actually are.

Is there a canon explanation of what they are talking about? If not, are there any particularly popular fan theories of what they are talking about?

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    Don't remember watching either episode (or the dialog got lost dubbing it for the German market; which often removes death and similar things when stuff is considered for kids), but any chance they're just talking about being forced into combat and the general "horrors of war" thing going on? Like seeing comrades being torn apart and killed left and right by robots that just don't care? – Mario Jul 16 '17 at 7:02
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AFAIK, there has been no canon confirmation one way or the other. The fan theory is that all clone troopers have nightmares about turning on the Jedi as a result of the 66-chip being in their brains. In both cases where "the nightmares" are mentioned, the other clones give each other a rather grim, knowing look.

Order 66 is not secret. It's part of the standing orders given to all clones. Its immediate predecessor, Order 65 covers doing the same thing to the Chancellor under the proper circumstances. The tactics for both would have been drilled into them repeatedly. (We first see that in S2's "Brain Invaders" where a company of clones taken over by Geonosian Brain Worms makes short work of Barris Offee and Ahsoka Tano. One clone goes so far as to openly comment "One thing we clones know is how to take down Jedi...")

What makes 66 different is that the chip would "cut out" the clones' higher reasoning ability and force them to comply utterly without question.

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