I liked this mission too, but I want to be able to now pursue quest lines where I oppose Section 31. I picked against them and want to continue picking against them, but I'd really like to throw down the gauntlet and start ferreting them out!
I went with Drake, because I believe in Section 31.
Would be curious to know what happens when you side with the Captain, but please send it to me via PM. Let's keep this thread spoiler-free to preserve the "holy $&%#" moment for people who've yet to do it.
yes, what is the major differences in the choices?
Nothing. You get different dialogs at the end, but I doubt that they'd make the game significantly different for people who chose opposing endings.
I wound up helping the captain. Despite my characters values being more in line with Section 31 (in a purely RP sense) Drake seemed more suspicious by his actions and the circumstances in which we came to meet (again). I found Drake the more likely suspect. And yes, when it was all over it was a "holy $&%#" moment. :p
Though I have to admit, I'm not sure whether I like or hate this Franklin Drake dude for putting me through all this crap over and over again... XD
Section 31 is your friend. Science and exploration and hugging cute cuddly alien puppy dogs in the sunshine is fine if you like that sort of thing, but the reality of the situation in interstellar relations, especially in 2409 where the federation is at war and everyone and his brother wants to see puppy hugging fed captains ground into dust and fed to targs, section 31 are the people that keep the wolves at bay.