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After Fate of the Jedi it's revealed that they formed cells on Coruscant after Abeloth's fall, and that they were still active on Kesh. But with the advent of Darth Krayt's empire and his conquest, did they remained isolated from Krayt, left alone, or integrated into Krayt's One Sith Empire?

That's........ actually a pretty good question. I can't recall hearing anything about them after abeloth. If they didn't join up with krayt, they may well be the only sith left in the galaxy at the end of the legacy comics.

There was suppose to be the Sword of the Jedi trilogy that got cancelled. I bet it would have explained their fate.

I bet with their leadership gutted, the Jedi hunted down the cells, and they were either isolated on Kesh, wiped out by the Jedi, or collapsed after their loss.

Krayt may have recruited a few of the more promising for intel purposes, but wouldn't want them en mass

Heck, I could even see him wiping them out as a potential thorn in his side, a large mass of non-loyal force users. That'd be ironic, bottled up by the Jedi til the Sith take over and wipe 'em out...

Ask Christie Golden.

I bet luke turns to the darkside in this movie