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They are seen as lizard creatures, then they are stunned with a phaser, brought back aboard Voyager, and seen next in human form back in sick bay. How did the Doctor do this?

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36  
Using the power of awful writing – Valorum Mar 4 at 14:46
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Ah, yes, the episode where they changed into lizards, mated, had offspring and then became humans again. The one the writers would sooner forget. – Wikis Mar 4 at 14:47
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If I recall correctly, they are transformed back during the commercial break. That was the last episode of Star Trek I ever watched. I sincerely hope it improved. – Eric Lippert Mar 4 at 16:54
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I was going to say they reversed the polarity of deflector array..... But I suppose they just reversed the polarity of the proton ray. That's almost the same thing..... – coteyr Mar 4 at 17:11
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@EricLippert I'm sorry that your patience didn't hold out. Later episodes were better. I believe this episode is widely recognized as the worst. Wikipedia's article on the episode shows the writer (Brannon Braga) of the episode called it "a royal, steaming stinker" (apparently ultimately quoting directly from an interview which is included in the DVD box set). Wikis's answer quotes Braga further. – TOOGAM Mar 5 at 5:01
up vote 28 down vote accepted

The Doctor used anti-proton therapy to erase all traces of the mutated DNA from their system.

EMH: I believe the answer lies in forcing his DNA to revert to its original coding. Once that occurs, his body should return to its former state. 

CHAKOTAY: How do we do that? 

EMH: We destroy all of the new DNA in his body. His cells will have to use the original coding as a blueprint. But the only way to destroy the mutant DNA is with highly focused antiproton radiation.

Later

EMH: I've eradicated all traces of the mutant DNA from your system and restored your original genome. Congratulations. You're human again. 

Unfortunately the same treatment won't erase all memory of this episode from my brain.

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18  
You can purchase a Tom Paris "Threshold" action figure. It comes with "three mutant offspring". – Praxis Mar 4 at 15:15
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@Praxis incredible! – Daft Mar 4 at 16:46
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@Praxis"Warning! Chocking hazard". I know I nearly did. – Nagora Mar 4 at 16:48
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@Praxis -- I love the way the price on the toy was cut from $7.99 to 3 for $10. That kind of says it all. – ThePopMachine Mar 4 at 17:06
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@Praxis Wow. I shudder at how ridiculous this toy is. I bet it was a real hit. – enorl76 Mar 4 at 21:17

In universe, from Memory Alpha

Paris and Janeway are reverted back to their Human selves using The Doctor's anti-proton treatments, although Paris is extremely embarrassed about having mated with the captain.

ie it was magic.

Out of universe, it was a sordid assault on rational thinking by a writing staff who should have known better1. From Memory Alpha again:

Brannon Braga named this episode as the one installment from the entirety of Voyager that he would "just as soon forget" and remarked, "That's a real low point [....] It really backfired on me. It was poorly executed by me."

1 And, to be fair, they did do much better for the rest of Voyager's seven seasons.

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Magic. Otherwise known as deus ex machina noun an unexpected power or event saving a seemingly hopeless situation, especially as a contrived plot device in a play or novel. – AntonChanning Mar 4 at 16:33
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"And, to be fair, they did do much better for the rest of Voyager's seven seasons." Which isn't saying much when it is literally impossible to do worse. :( – Shane Mar 4 at 17:26
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What was the reasoning for even entertaining such a horrible plot and then going forward with the week's worth of shooting to turn it into an actual episode?! Isn't there a point where you look at it and call a time out? – enorl76 Mar 4 at 21:18
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@enorl76 That's a great idea, except that it would have disrupted the shooting schedule for the next episode. I do wonder, though, how many people this particular train wreck had to get past to find a green light... how many people didn't think it was stupid. – T.J.L. Mar 23 at 12:24

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