The Mudd Incident was conceived by Star Trek Into Darkness screenwriters Roberto Orci and Alex Kurtzman. Explaining where the name came from, Kurtzman stated, "It's kind of necessity is the mother of invention. We knew that for the mission that Kirk wants to go on to work, it couldn't be a Federation ship. So why the hell would the Enterprise have a non-Federation ship on board? 'I got it! The Mudd incident!" Given the fact that the name constitutes an in-joke referencing Harry Mudd, Orci admitted, "I still have a giggle about [writing that line] now." 
In the comic book Star Trek: Countdown to Darkness (co-written by Roberto Orci), the Mudd Incident had Kirk uncovering a civil war on a pre-warp world where the aggressors were being given weapons by the Klingons, while the resistance were aided by Robert April and Mudd (β), the Bajoran daughter of Harry Mudd. Mudd's ship and its cargo were brought on board by Uhura, who had the command chair. AdmiralPike informed Kirk that any mention of April or his actions was strictly classified.