The verb "to kill" can mean figuratively
I have not seen the movie, so I don't know if your context is negative or positive. Just looking at the sentence, the first character is clearly threatening the second (though not necessarily with real death - people can say "I am going to kill you" just when they are really angry with someone). The second character turns it into a joke, and uses another meaning of the verb "to kill".
So, if the context were positive (with no intention of real killing), your sentence may mean something like
I am going to make you pay for this! (or I am going to make it hard for you)
You have already annoyed me to death/gotten on my nerves/harmed me.