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The Commander was an Auton posing as a Roman commander, whose appearance was based directly on Amy Pond's memories of a book she owned on Romans (Which was a trap for The Doctor). He was stationed near Stonehenge by the Alliance and decided to help the Eleventh Doctor. He later placed the Doctor in the Pandorica when his Auton programming took over. (DW: The Pandorica Opens) When the Doctor negated the cracks in time, the Alliance was never created and thus the Commander never existed. (DW: The Big Bang)