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In the Star Trek Discovery Episode S1:E7 Magic to Make the Sanest Man Go Mad - how did the crew regain control of the ship from Harry Mudd?

I understand the logic behind re-wiring the Captain's Chair, but they also use the Transporter at the end of the episode without making any mention of regaining control of the ship from Mudd.

Of course, I'm not referring specifically to the Transporter. How did they regain navigational control and vocal control of the computer (things they were denied access to moments earlier).

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    I thought someone made a comment about only critical systems being hijacked. – Darren Nov 27 '17 at 17:02
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Unfortunately, the show very explicitly skims over this. Burnham kills herself and buys one more iteration; once she does, we have a super quick montage that really only shows us a few crewmembers whispering intensely to one another.

I think the implication is that Stamets' efforts to establish a "chain of trust" would have paid off sooner or later. That he became capable of persuading Burnham to help, and learned what guidance to give her and the crew (e.g. for Tyler to set up security mechanisms). And that they were already really really close to being quick enough to block Mudd's takeover -- one last time, and everything worked.

Alas, this does seem to imply that Stamets cracked and gave the ship up to Mudd at pretty much the worst, stupidest moment possible.

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After Mudd left the ship they could work on the computer systems to reset them. They couldn't do it during the takeover because, once everyone was brought up to speed on what was happening, Mudd was already in the system and they only had a few minutes to do anything before the loop would reset. Once he was off the ship, they had all the time they needed.

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