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Alex Hopkins was the leader of Torchwood Three in 1999. He murdered the entire team except the immortal Jack Harkness.
On New Year's Eve 1999, Alex gathered the Torchwood Three team in the Hub, except for Jack, and killed them. Jack arrived to find the carnage. Hopkins then shot himself. With everyone else now dead, Jack took over as leader of Torchwood Three. Hopkins had killed himself and the others as he saw the team unprepared for upcoming dangers in the 21st century. He spoke of a storm coming which humanity could not face. (TV: Fragments). The two bodies Jack discovered were James Unsworth and Karen Baldwin. (AUDIO: Red Skies)
Under Torchwood policy, Hopkins' remains were presumably put into permanent storage in the Hub, although whether the morgue survived the destruction of the Hub during the 456 incident is unknown. (TV: Children of Earth: Day One)