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I just completed the second mission, and killed all of 2 NSF, one who was running for an alarm, and another who I could not avoid or tranquilize without notifying others and sounding an alarm. For some reason, the game is now acting like my character, who I have been playing as conflict averse but willing to kill if no viable alternatives exist, is some kind of bloodthirsty monster. Why is that? Are there any similar situations later on in the game, or is this an isolated incident?

Also, beyond interactions with certain characters, does killing have any impact on the game's story, primarily the ending?
This question / problem has been solved by CDJ75image
This was discussed in another thread recently, but yeah, the "JC is a dick" detection is somewhat broken in Castle Clinton, basically if you go near the main entrance the game will assume you went in guns blazing...and even if you take the back entrance, as soon as you take up the stairs near the ambrosia barrel...the game assumes you killed everyone.

In your case it's a moot point though because you DID kill 2 guys and the game only accounts for two outcomes with Castle Clinton.

I wouldn't say there's any kind of morality system in this game in that there's no good/evil scale and if you do lots of good things npc's react different to you over time...it's more like every action you take has a direct effect on something regardless how you behaved prior.

In Castle Clinton's case it just effects a few conversation during your next HQ visit and Carter won't give you extra ammo.

The ending is solely decided based on which mission objectives you complete during the last 15 minutes of the game.

Killing people affects certain details but nothing will change the story on a large scale. By the way, after the first Hell's Kitchen mission the game doesn't even differentiate between knockouts and kills aside from the bodies description...
Post edited November 01, 2012 by CDJ75
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CDJ75: Killing people affects certain details but nothing will change the story on a large scale. By the way, after the first Hell's Kitchen mission the game doesn't even differentiate between knockouts and kills aside from the bodies description...
Huh... Odd, that. Oh well, at least I don't have to worry about starting my character from scratch. I trained him in lockpicking, computers, and electronics, and got him up to advanced in pistols, relying on non-lethal means as much as possible and and falling back onto the laser-sighted stealth pistol to land double tap headshots if all else failed. Would suck to have to ditch all that.
It doesn't have anything to do with the entrance you take, it's the fate of the NSF troopers. In the vanilla game, ALL of them must be KO'd for the check to consider JC as having been merciful. That also includes not allowing Anna and her backup to kill any of them. The community patch efforts (v2.0 and G-Flex's Human Renovation) fix it so that the check only considers what YOU did.

EDIT: So do Shifter and its' derivatives, but I wouldn't suggest those for a first playthrough.
Post edited November 02, 2012 by boct1584