Jhamin said:
*Pick a random guy to frame as a Cylon so I can cover my but while pointing out the cylon thingie (which was never mentioned again). How big a jerk am I for selling out an innocent? Oh wait, I guess he really *was* a Cylon so it all worked out. (OK, so it was Baltar. But now he has unknowing done a good thing for the wrong reason. IF you want him flawed, let him be.)
Ah, but that's the beauty of it. At first, he talks about using the guy as a scapegoat and the next thing you know, he's explaining to Tigh about how he took skin samples and analyzed them to look for the trace elements they found after the cremation of the Cylon from the station. They leave you for the rest of the show thinking Baltar is a rat who used this guy as a scapegoat and made up all that stuff about the test. Then, in the last scene, you find out he really is a cylon. Now, you have to wonder if it was just blind luck he stumbled on an actual cylon as his scapegoat or if he really did find a way to detect cylons and was on the up and up the whole time.
There are a couple of other moments like this where you wonder if Baltar did/was about to do something bad or if he genuinely had good intentions all the time.
Baltar finds himself in a real fix. He's not a traitor and doesn't want to be one, but his past and present association with "6" puts him in a situation where it would be really easy for people to decide he is one. He knows he can help out, especially with the info he's getting from "6", but he's trying to do so without revealing the things that would make others see him as a traitor. Its true that he looks out for himself before anything else and that helping the fleet out is helping himself out, but I don't think that's his only motivation. I believe he genuinely wants to do the right thing and help people out, just not at the cost of his own life.
Why does he feel responsible? We know that "6" was playing him like a piano, but he also knows he broke the rules for her. Evidently, she wasn't supposed to have the access she did. Rather, he shared his with her so she could help with his program. Some things were said in one of the scenes on Caprica that lead me to believe that some of it was aimed at helping her secure future defense contracts as well. I got the impression from his comments about computer technology during his interview on Caprica that he didn't believe the cylons were comign back anytime soon. He was playing fast and loose with the rules, but I don't think he was an intentional betrayer of humanity. Rather, what he thought was a victimless bending of the rules to gain financial advantage and get in good with his girlfriend turned out to open the door to apocalypse. Because he isn't an evil man, he feels immense guilt about that.
I may have the chronology wrong, but I think the "cylon thingie" was mentioned again. I'm pretty sure the scene where the bridge officer is explaining how he noticed it and thought it was part of the museum setup was after the cylon was arrested.