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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) he, as of Torchwood Series 3, has returned from Africa and is on his honeymoon with Martha
In Series 3 of Torchwood, Martha Jones is mentioned to be on her honeymoon, which explains her absence during the series and possibly reveals that Tom has returned from Africa
In The Next Doctor one of the men Ms. Hartigan keeps alive is named Mr. Milligan. It is unknown if there is some relation such as with Gwen and Gwynith.