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Thomas Milligan was a doctor who worked for the NHS in 2008. When the Master brought the Toclafane to Earth he became a fugitive. In 2009 during the Year That Never Was, he met Martha Jones when she returned to England and took her to see Professor Alison Docherty. When the Master tracked them down, he used his laser screwdriver to kill Thomas.
When the Master's Paradox Machine was destroyed, undoing the Year That Never Was, and reversing time back to 2008, Martha phoned doctor Thomas Milligan, and then hung up, so that she could reassure herself in that in this timeline, he was alive. (DW: Last of the Time Lords)
When Martha, now working for UNIT, joined Torchwood 3 temporarily as a medical officer, she mentioned to the flirtatious Owen that she had a serious boyfriend. (TW: Reset) In fact, she had a relationship with "Tom", suggesting that she had initiated a relationship with Thomas Milligan. (WEB: torchwood.org.uk)
Martha later got engaged to Tom who is now a paedatrician working in Africa. (DW: The Sontaran Stratagem)
When the 456 attacked Earth's children, Martha Jones was mentioned to be on her honeymoon, which explained her absence during the crisis and possibly revealed that Tom returned from Africa. However, it was unclear whether this was a honeymoon with Mickey Smith, or in fact she married Tom. (DW: The End of Time)
"It is unclear how the relationship between Martha and Tom broke down. Giving that Martha was willing to leave the Doctor for good to marry Tom, it is likley that he died when the Daleks stole Earth.