The origins start in the mentioned anime series. The meme begins with the antagonist turning from plead to hostile. The main character then says "Omae wa mou shindeiru" (This translates into "You are already dead"), then followed by a response of the meme: "Nani?!" (Which translates into "What?!"). This is soon followed by the death of the antagonist. Similar events are seen throughout the anime series.
The meme is used by internet by an attacker and a victim. Simply put, the attacker attacks the victim, which is followed by a pause and the audio effect of the meme, then the resuming of the clip.