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- For individuals with similar names, John Smith.
Jonathan Smith (quite possibly an alias) was the name used by a member of the Supreme Alliance in 1889 England.
Biography
Smith, an expert on zygma beam radiation, had, in his native time on the planet Biblios, acquired a diary entry by H. G. Wells describing the death of the Doctor at the hands of Smith himself. He had also the knowledge needed to restore the disfigured and dying Magnus Greel to health.
Smith planned to rescue Greel before an earlier incarnation of the Doctor could defeat him. Travelling back in time using zygma beam radiation to the 1880s, he posed as a graduate of Cambridge University and presenting himself as a physicist of his adopted era, he strategically befriended Wells. The Doctor had forged the diary entry so that Smith would find it in the 51st century, setting up Smith's capture by the Torchwood Institute. Torchwood, as the Doctor had planned, mistook Smith for the Doctor himself, using his usual alias John Smith.
The Doctor believed that Smith would be released and face trial in his native time once Jack Harkness would join Torchwood and make them realise he wasn't the Doctor. (IDW: The Time Machination) However, Smith was dissected before this could occur. (IDW: Final Sacrifice)