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Fair warning - Lots of old spoilers in this narrative

In the rebirthed Doctor Who, S03E02 “The Shakespeare Code“, the Doctor and William Shakespeare manage to trap the three witch-like Carrionites in their own crystal ball.

The rest of the Carrionites and all the copies of 'Love's Labour's Won' were sucked back through the closing portal and as the Doctor, Will Shakespeare and Martha Jones are sitting on the deserted stage during the episode wrap-up, the Doctor picks up the crystal ball imprisoning the original three witch/Carrionites and says,

Anyway, it's time we were off. I've got a nice attic in the Tardis where this lot can scream for all eternity.

Then Queen Elizabeth shows up and retro-remembers the Doctor (as a spurned lover or jilted bride); the Doctor clearly tucks the crystal ball into his coat before running off and escaping in the TARDIS.

I can remember the head of a Cyberman being used as a compass or homing beacon in a later episode but that endeavour went pear-shaped in quick order. I also remember the TARDIS being used to transport the Margaret Blaine Slitheen but she turns into an egg. I don't recall any other bad guys or gals being imprisoned long term.

Have there been other cases of the Doctor keeping villains imprisoned in the TARDIS for an appreciable length of time (between two episodes up to and including eternity)? Original series, interim movies and rebirth responses apply.

Edit:

There is evidence that the Doctor was willing to do this at least one more time but things didn't work out.

At ~00:39:35 in S03E13, Last of the Time Lords, there is this exchange of dialogue:

Master: You still haven't answered the question. What happens to me?
Doctor: You are my responsibility from now on. You're the only Time Lord left in existence.
Captain Jack: Yeah, but you can't trust him.
Doctor: No. The only safe place for him is the TARDIS.
Master: You mean ... you're just going to keep me ...?
Doctor: Hmm, if that's what I have to do. <to Captain Jack> It's time to change. Maybe I've been wandering for too long. Now I'll have someone to care for.
<a shot rings out and the Master falls to the ground>

The Master appeared to refuse to regenerate but was never confined within the TARDIS. This would not qualify.

At the end of S03E11 - Utopia, the Master takes control of the TARDIS and abandons the Doctor, Martha Jones and Captain Jack Harkness at the end of the universe. This shouldn't be considered imprisonment of a villain.

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    For any length of time? Wouldn't that include episodes where he gets the baddie into the TARDIS just during the episode in order to defeat it before the end? (I can't recall any such episodes offhand, but doubtless there are some.) How about restricting it to "keeping villains imprisoned in the TARDIS beyond the end of the episode / resolution of the crisis", which seems to be more in line with what you're looking for?
    – Rand al'Thor ♦
    Aug 28, 2019 at 7:24
  • @Randal'Thor - At least two of the baddies in the aborted salvage operation episode could be considered real baddies. I was thinking of that episode when I wrote this question. They only encountered different dimensional or different timelines of themselves. However, I take your point. I was inferring something through 'imprisoned' that should have been made more clear.
    – user62584
    Aug 28, 2019 at 7:36
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    Another interesting case is House from "The Doctor's Wife". Was it completely destroyed in the end, or was its consciousness simply subdued by Idris / TARDIS, meaning that it might still exist in some form trapped deep within the TARDIS's consciousness?
    – Rand al'Thor ♦
    Aug 28, 2019 at 7:40
  • @Randal'Thor - Given the animosity between Idris / TARDIS and HOUSE, I would speculate that they couldn't coexist in any pocket universe.
    – user62584
    Aug 28, 2019 at 10:49
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    @Jeeped It wasn't The Doctor's first intention for Tzim-Sha though, was it? At their first encounter, she mercifully sent him back to where he came from and chastised the guy who kicked him off the crane. This is more in line with the Tenth Doctor's character who gave "one warning" and then anything he did after that were a consequence of their own doing.
    – Astralbee
    Sep 3, 2019 at 11:36

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A number of Cybermen entered the TARDIS in the Sixth Doctor serial "Attack of the Cybermen". At least one of them does not have an onscreen death scene.

http://www.bbc.co.uk/doctorwho/classic/episodeguide/attackcybermen/detail.shtml

If you accept comics continuity, a demonic being named Magog got trapped in the TARDIS and remained there until at least the Doctor's seventh regeneration.

https://tardis.fandom.com/wiki/Magog

Also, not quite what you probably mean, but in the alternative continuity story "Scream of the Shalka", a version of the Master has become an ally of the Doctor and can't leave the Doctor. This version of the Master may or may not secretly wish the Doctor (and universe) harm.

https://tardis.fandom.com/wiki/The_Master_%28Scream_of_the_Shalka%29

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