Before becoming a missionary with the China Inland Mission (CIM), Cooper was Secretary of the Y.M.C.A in Gourock, Scotland. “He received his call to missionary service through reading a copy of a sermon by C.H. Spurgeon, entitled ‘The Divine Call for Missionaries.’” (Martyred Missionaries, 156.)
He reached Shanghai on January 9, 1881, and proceeded immediately to Anqing, Anhui, for language study. He made rapid progress, and shortly was taking part in the regular work of itineration from the missions station in Anqing to the six outstations in surrounding villages.
In September, 1882, he was stricken with typhoid fever, from which he did not recover until two months later. His hearing was permanently damaged by this illness.
He was appointed in 1884 to serve at Wuchang, Hubei, where he worked for about as year. After that, he returned to Anqing, Anhui, were he was made supervisor of the CIM work there, including the church and men’s training home. He was later given the task of advancing the CIM work in all of Anhui according to Nevius’ formula for establishing self-governing indigenous churches. 1885 the Anqing church was organized according to these principles, with Cooper as adviser. In 1885, along with nine other senior workers, he was made a member of the CIM China Council, and was described as “the member ... whom Hudson Taylor valued more than all.” (HTCOC 7:97).
He returned on furlough in England 1887 on the same ship as Hudson Taylor and married a girl who had gone out to China the year he had; Hudson Taylor conducted the wedding. Cooper sailed in 1888 for China with her and their first child. On the voyage, he became desperately ill, so that his life was feared, but he recovered. Upon his return, he was appointed Superintendent of the CIM in Anhui, stationed in Anqing.
In 1893 (1894?), after the CIM had grown much larger, he was appointed Assistant Deputy Director under Deputy Director John Stevenson, and moved to Shanghai to take on administrative duties, especially all correspondence that was not directed to Taylor or Stevenson or marked “private.” He was thus in line to take over from Stevenson in time. He clearly had “won Hudson Taylor’s profound confidence and was being groomed for leadership at the highest levels.” (HTCOC, 7:200) At times, when Stevenson and Taylor were both absent or ill, he served as Director; Taylor trusted him completely. “He did everything well and made no mistakes.” (HTCOC, 7:246) It was difficult for Stevenson, whose brusque leadership style alienated many, to delegate authority or to treat Cooper as a “junior partner” rather than an inferior, but the godly Cooper endured this patiently. He was ably assisted by C.T. Fishe.
He took a second furlough in England in March, 1898, returning to China the following October, after spending two months in Canada on the way. Those who met him there spoke of the powerful spiritual impression he made upon them.
As opposition to Stevenson grew, members of the London Council urged Taylor to appoint Cooper as Taylor’s second-in-command, to succeed him when he retired from active leadership. In 1899 or early 1900 Cooper was appointed Visiting China Director to deputize for Hudson Taylor and to “travel extensively trouble-shooting and encouraging front-line missionaries,” with full power “as China Director to do what is necessary,” and was apparently being considered by Taylor as his successor as General Director. One critic of Stevenson described Cooper’s “apparent fitness for dealing wisely and well with whatever may come before him,” and thus his suitability for greater authority. (HTCOC, 7:276, 312) Taylor’s intention was that “Cooper, as an equal partner with Stevenson in responsibility in China, was to have supplied the personal touch, the sympathy and understand that the dour Scotsman [Stevenson] did not lack but found hard to show. As travelling director Cooper was to get close to the men and women of the outback, see their circumstances, listen to them, sense their spiritual morale, and give them advice and support.” (HTCOC, 7:441)
He was often plagued with poor health, in addition to his impaired hearing. Respiratory troubles frequently forced him to take a complete rest from ministry. On his last furlough in England, “he was run over and seriously injured, being taken home almost unconscious.” (Martyred Missionaries, 156).
In 1900, he had detected the coming danger to missionaries when the Boxers killed Elder Si of Hongtong, the successor to Xi Shengmo, Shanxi. He had traveled through Baoding to Shanxi, visiting mission stations on the way, reaching a group of thirty-two missionaries in conference at Linfen (Pingyang) on May 17. Accordingly, at the conference he spoke on Hebrews 13:5-6. From there he went to Lu’an (now Changzhi), Yuwu and Lucheng, speaking to Chinese Christians and missionaries on the same theme of confidence amidst danger. “The keynote of his message was the likelihood of the churches in China being called upon to suffer for Christ.”(Martyred Missionaries, 77) He also described the change in the Apostle Peter between the time that Jesus warned him of the coming cross and his later references to sufferings in his sermons and letters. Another missionary wrote, “Mr. Cooper’s messages were full of comfort and strength; especially so were his thoughts on the words: ‘I will never leave thee, nor forsake thee. So that we may boldly say, “The Lord is my helper, and I will not fear what man shall do unto me.”’” (Martyred Missionaries, 103)
He had intended to return south through Henan, but was needed by CIM Deputy Director John Stevenson in Shanghai, so he headed towards Baoding, Zhili, with Tianjin and then Shanghai his destination. Instead, he walked into the center of the Boxer Rebellion. In Baoding he stayed with Mr. and Mrs. Bagnall, who were in charge of the CIM business office.
On June 30, Boxers attacked and burned the Presbyterian missionary premises, killing all inside, including faithful Chinese helpers who had chosen to stay behind. The property and missionaries of the American Board were next assaulted. One missionary was killed and two women taken captive. Hearing of this, Cooper and the Bagnalls hurried to the imperial military camp nearby, hoping for escort to safety. Instead, they were handed over to the Boxers, tied to each other, and led out for execution. All were beheaded, and their bodies exposed overnight before being thrown into a common grave.
Cooper was described as “a quiet, saintly, but physically powerful and mature man.” (HTCOC, 6:386). “One of the very blameless lives that I have ever come into contact with,” wrote one friend who had been with him amidst very trying circumstances. (Martyred Missionaries, 156) “He could be perfectly firm and decided when such an attitude was called for, but he could say ‘No’ in such a way as not to give offence to those with whose proposals he was unable to agree.” (Ibid., 157). “Quiet strength, gentle patience, frank faithfulness, and tender sympathy” were qualities which exercised a profound impact on all those with whom he came into contact. (Ibid.)
He was survived by his wife and children.