It became famous as a euphemism, supposedly used by the CIA, meaning "to kill" or "to assassinate." It's sometimes used in a kind of nasty, joking way, because it is such an evasive way of saying "kill."

I'm not sure what you mean by "how is it used differently now", but the term "(terminate) with extreme prejudice" and its history is described quite well here: https://en.wiktionary.org/wiki/terminate_with_extreme_prejudice You'll most likely come across this term in movies and TV.