I've started as dwarf technologist and, while doing usual business at Shrouded Hills, I messed up bank robbing quest.
I just stole safe password from Jacob, forgot to take quest (I was thinking about Jayna) and went to Dernholm. After returning I wanted to take this quest but Jacob is accusing me in robbery!
Now Doc stands at the entrance and attacks me on sight.
If I kill him, would I get bad reputation in Shrouded Hills?

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I didn't find any bad reputations given to you if you kill him in the Arcanum files.

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"Violence is glamor, i'm glamorous"

yes you will get the outlaw reputation in shrouded hills .

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Nasrudin sent me to kill Arronax too bad turned out to be ................... alas!!!!

My experiences conicide with Wims'. I didn't strangely enough get a bad reputation from killing Doc Roberts because of this, the only trouble is he can be hard to kill!

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The chemistry must be respected.

As far as I know killing only Doc Roberts won't give you a bad reputation as long as the crime is not witnessed. Otherwise you will end up fighting the whole town and be known as the butcher of Shrouded Hills. If you are seen to rob the bank then you will receive a bad reputation as well.

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The thing is that I have reputation of bank defender, it's just that I forgot to take quest and rat on Jacob afterwards.
Also, I'm planning to include all possible dwarf followers in my party.
The problem is Jormund.
Does he have unique dialog lines or he will be useless equivalent of Jayna?

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Jormund falls in the same category as Jayna when it comes to interactivity after the initial recruitment.

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Where we're going, we won't need eyes to see.

Having 94 fatigue points and Disintegrate and Body of Fire as a dwarf is quite unique though.

The regular fainting fits are almost worth the uselessness.