None of them had recognized anything was wrong until they did not come out of hyperspace when they should have. After that they wanted to attempt to rip the navigation system apart, but discovered that the command decks were sealed off. They tried cutting through the doors, which eventually worked, but discovered there was nothing they could, unless they wanted to shut down their hyperdrives, in a fashion which did not permit restarting them
As they hadn't been dropped in a star, nor did they have any other FTL capability and comms had not yet been installed, that left them with very few options. Waiting until they got to their destination and trying to deal with whatever awaited them there was the best of those, very poor, options.
Eventually they arrived in the middle of nowhere. It was not a star system, there were no comets, or other astral objects which might act as a guide and their minimal weaponry was shut down, as were their sublight engines. The techs instantly began work on their ship, working on disconnecting the override and reprogramming the infected areas. The two empty ships sat there. The Ugnaughts were very clever, but thirty some techs were doing rather better than the two of them, especially as they'd been trapped in recriminations and acrimony for most of the trip.
None of them saw the bots spreading out from the cloaked station. But they did hear the sound of metal footsteps as droids boarded their ships. Their first assumption, that they'd been found by their fellow Separatists was belied by the droids design. It was nothing like the standard models in service with the Separatists. Within moments they were all restrained and stuffed into a shuttle.
XXX
The Duros officer saluted the massive bot which filled most of the command deck. "Commander, we've completed pharmacological interrogation of the prisoners, as well as a memory drain. I have completed my review of the evidence and believe there is sufficient proof to support a conviction for slave trading and use of slave labor by all parties, as well as multiple counts of murder, for several of them, as indicated in my report. I request permission to present these charges to the Court Ultimate and seek Execution Warrants for them."
"Permission granted. You've also sent the information and their physical details to the Eyes?"
"Yes, commander. I understand we can expect surgically altered agents here shortly. The ships are to be kept here until they arrive, then turned over to the new agents."
"Understood. We serve the Union."
The officer saluted again, "And defend the Bastion," he turned on his heel and marched off.
The commander nodded to himself. Some things still had to be done orally, including certain requests. Bringing charges before the Court Ultimate was one, reporting other things was not, but organics needed to speak and the commander made concessions to the needs of his organic officers, such as pretending he needed a body, rather than being embodied by the covert station that surrounded them, or adopting some humanoid mannerisms. Some of his synthetic troops did not appreciate that. The most recent generation had shifted their chassis designs to the abstract, distinct from any form organic life naturally took, but the commander had held his post for more than three centuries and didn't bother paying attention to such fashions anymore.
So long as everyone did their duty to the Union and the Bastion, he could ask nothing more and would accept nothing less.
XXX
"This is ridiculous, we are soldiers of the Confederacy of Independent Systems, you have no authority over us!"
"By the order of the Court Ultimate, by the evidence of your own memories, by the testimony of your own words, you are guilty of engaging in the slave trade. You are guilty of forcing others to labor on your behalf. You are guilty of crimes against the ideals of the Bastion. The Court Ultimate is a court of universal jurisdiction. At this time we grant you an opportunity to make a statement to be recorded and included in the records of your execution," the Duros man said, his dark green uniform unflatteringly contrasting with his blue skin.
"Execution? For what?"
"Did you not understand the charges?"
"Look, I just went where I was told and did what I was told. You want the Ugnaughts, or Count Dooku, or someone else."
"Do not worry, justice will come for them as well, in the fullness of time. Do you have anything else you wish to say?"
The tech then attempted to filibuster her own execution. The soldier explained that there was actually a time limit on last statements and the matter descended into blubbering and pleading before a single shot to the head ended things. The man looked to the shadows where a woman wearing the same face as the tech waited. "Did you get what you needed?"
"I believe so. Thank you, officer."
"The Shield of the Bastion is always eager to assist the Eyes, however we may."
"Appreciated."