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Thomas and Martha met during her journey to save the world in the season 3 finale of Doctor Who, Last of the Time Lords. After time was reversed at the end of the episode, Martha found Tom; he was a pediatrician working in Africa. They began dating off-screen, and in the fourth episode of season four, The Sontaran Stratagem, it is revealed they are engaged to be married (which Martha seems to be very excited about).

DONNA: She's engaged, you prawn.

DOCTOR: Really? Who to?

MARTHA: Tom. That Tom Milligan. He's in pediatrics. Working out in Africa right now. And yes, I know, I've got a doctor who disappears off to distant places. Tell me about it.

Then, out of nowhere, it is the last David Tennant/R.T. Davies episode The End of Time special and Martha is married to Mickey!

Did R.T. Davies or Steven Moffat ever address or explain what happened?

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  • Moffat hasn't mentioned it since he has generally left the RTD era to Davies, whilst Davies hasn't mentioned it either in any interview after an extensive search on Google. I'd speculate that Mickey and Martha were quickly married as they were part of the 10 Doctor's "goodbye" and probably fit well into the script.
    – VirtualByte
    Nov 16, 2015 at 21:25

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You are correct: Martha's breakup with Tom and subsequent relationship with Mickey is never covered in canon prior to the announcement in The End of Time that Martha and Mickey are married.

The closest we have is the following remark by Jack Harkness in the Torchwood radio special Lost Souls (emphasis mine):

MARTHA JONES: (communicator) Jack, I need you.
CAPTAIN JACK: Don't tell me, you've finally seen the light and dumped that fiancé of yours. I'm on the first train to London.
MARTHA JONES: (communicator) I'm not in London, I'm in Switzerland. Have you heard of CERN?

Martha doesn't respond to Jack's remark. It could be just the normal Jack Harkness flirting, or it could suggest that something is wrong in her relationship with Tom at this stage.

Out of canon, you can find LOTS of speculation about Martha, Tom, and Mickey on this discussion thread.

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