It's likely a threatening or warning phrase, suggesting that the speaker is serious and might take action if the person being addressed doesn't comply.
Well, in this fanfic, 'Don't make me come and get you' could imply that the speaker is frustrated or impatient and is warning the other character that they'll have to intervene forcefully if needed. Maybe the person being spoken to is not doing something they should be or is in a dangerous situation.
In the 100 fanfic, 'Don't make me come and get you' usually indicates that the speaker is at their limit and is prepared to take direct action to get the other person. It could be out of concern or anger, depending on the context.