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Just curious if there's any info on this issue in Star Trek: Into Darkness since it wasn't explained in the movie. How did Khan know that the Enterprise warp core had problems? Was there some document from Section 31 (or whatever that secret MI-5 type Starfleet organization is called) that Khan might have come across where this type of sabotage is their M.O.?

I know it wasn't explained in the movie but maybe there's some sort of answer from the Star Trek universe I haven't read/found yet.

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    I'd say it was just a very safe guess (especially for someone as intelligent), as Khan knew that Marcus wanted to start a war with the Klingons and wanted the Enterprise to provoke that war. So sabotaging the warp core was the best method to keep the Enterprise from leaving the Klingon space.
    – Napoleon Wilson ♦
    Apr 11, 2015 at 11:35
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    It's just common knowledge...like knowing your VW Camper is going to have transmission issues...
    – DA.
    Sep 21, 2015 at 0:16

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Like you said, there's no indication in the film that Khan actually knew the Enterprise' warp core had malfunctioned. However, the dialogue during the scene in which Khan is first spoken to in the holding chamber, seems to show us why he could assume this:

Khan: Why aren't we moving captain? An unexpected malfunction, perhaps in your warp core? Conveniently stranding you on the edge of Klingon space?

Bones: How the hell do you know that?

The fact that the ship wasn't moving (assuming Khan could actually tell) was a fairly good indication that the ship had no warp capability, since the ship was in enemy territory. Also, Bone's response would immediately confirm Khan's statement if he was only bluffing.

Just as Napoleon said, he was probably guessing, and it would be a safe guess. But I think the fact that he knew the ship wasn't moving was enough evidence to convince him that the warp core was failing.

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