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The Prisoner - Introduction
You can start this quest at any point by going into the terminal at Camp McCarran. On the second floor, in one of the side rooms, you can find Lt. Boyd keeping watch over a prisoner. It seems that they captured a high ranking member of Caesar's Legion, but he doesn't want to talk. Since you're an outside contractor, you can apply some "enhanced Interrogation" techniques to Silus to make him talk without technically breaking any NCR rules.
Of course, if you want to support Caesar's Legion, you will want to hold off until you've met Caesar. That opens up an interesting course of action.
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The Prisoner - Breaking Silus
If you want to help the NCR and Lt. Boyd, you can just follow her wishes exactly. Just use the non-speech checks and beat Silus up after he decides to clam up. He won't fight back, so just hit him a few times until he loses about half of his health. Boyd will make you take a break and step in to intimidate him more. You'll get sent back in a second time to finish softening him up and complete the quest (as long as you don't accidentally kill him).
Note that if you plan to fight him, you should probably have ED-E wait somewhere. ED-E has a nasty habit of rushing in and using its laser, which has the chance of messing the signals up.
There are also some unmarked Speech and Intelligence options. It seems that having 8 points in Intelligence will allow you to convince Silas that you're a Caesar's Legion assassin who infiltrated the base. If you follow the path, he'll confess a lot of information and you'll be able to crush his spirits at the end by exposing your lie. A similar path for Speech, requiring at least 50 points, allows you to just talk him into confessing. Note that one Speech option just gets him to attack you, which is more of a moral issue than a practical one.
You should also be able to sneak a knife into the room through a companion (especially Boone, since Boone wants to kill the prisoner) and use that to kill him easily.
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The Prisoner - Help Him Escape
If you have met Caesar, you can tell Silus that you're on his side and you'll help him escape (in a whisper of course). You'll have to rough him up to keep up appearances, but the plan will kick in after Boyd takes you out of the room. You should be all alone in the waiting area while Boyd intimidates Silus. Look into the lockers on the side wall and steal the silenced pistol. This will count as a holdout weapon for the next time that you go into the room.
Use the conversation command to give the silenced pistol to Silus. He'll do one of the worst performances of being unconscious, but Boyd will buy it. Walk out and just hang around for a moment if you want to see the plan in action. The soldier that goes in after Boyd to escort Silus will get shot in the head. Silus will then steal his uniform and calmly walk out of the base in his disguise. He'll be able to get out of the base and no one will know that you were responsible for the escape.