The Mudd Incident was a invent in which the USS Enterprise was involved in 2259 prior to its mission to Nibiru. (TOS - Countdown to Darkness comic: "Number Three"; TOS movie & novelization: Into Darkness)
Prelude[]
In 2239 of the Kelvin timeline, the USS Enterprise under Captain Robert April did a routine survey of Phaedus IV and it's inhabitants. There, April saw a genocidal civil war being fought by a group that called itself the "Shadow" against non-shadow. In that moment, April decided to help the non-shadow. He then worked with XO, Alex Marcus to fake his death. (TOS - Countdown to Darkness comics: "Issue 1", "Issue 2")
April took many weapons and technology with him to help the non-shadow fight back despite him violating the Prime Directive. Marcus ensured that supplies arrived from Section 31 through the trader Mudd. For over two decades, April and the non-shadow fought the Shadow. During this time, April then discovered that the Klingon Empire was supplying and backing the Shadow. During this time, Marcus had become the Commanding Officer of Starfleet Command and leading member of Section 31. He ensure that his control program built into the new USS Enterprise. Marcus then arranged for the Enterprise to do a survey at Phaedus. Marcus also awakened former augment dictator, Khan Noonien Singh (under the alias "John Harrison") to build ships and weapons for him. Marcus knew that April would able to distract the Klingons by giving the Enterprise. (TOS - Countdown to Darkness comics: "Issue 1", "Issue 2"; TOS movie & novelization: Into Darkness; TOS - After Darkness comic: "Part 1")
The Enterprise's arrival[]
In 2259, the Enterprise under Captain James T. Kirk arrived at Phaedus under orders from Admiral Christopher Pike to do a survey. However, Kirk and his crew detected a energy fluctuation coming from the surface. (TOS - Countdown to Darkness comics: "Issue 1", "Issue 2")
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