Hostilities recommenced on the northern border (Cape Colony) in January 1879, and subsequently in Bechuanaland and the Keate Award, and the Griqualand West forces were ordered to co-operate with those of the Cape Colony. On 11th February Warren was appointed Acting Administrator of Griqualand West and disarmed all the natives. During this and the following month the whole country was disturbed in consequence of the disaster at Isandhlwana, and Warren offered to take 500 white troops to the assistance of Lord Chelmsford, but it was not considered desirable to take 500 white men away from Kimberley at so critical a time. As Special Commissioner Warren inquired into the land question of the Bloemhof districts, and in April commanded the Griqualand West Field Forces in the northern border of Cape Colony, and made arrangements to prevent the rebels breaking through again into Griqualand West. They were thus forced into Bechuanaland, and in conjunction with the Bechuanas again threatened Kuruman. The Bechuana and Griqua ringleaders and the Cape Colony rebels were defeated and captured by the Griqualand West forces in August, and Warren was able to reduce the strength of his columns in the field. He was invalided home in the autumn on account of the hurt he sustained from the falling tree. He left the Cape much to the regret of the South African people, among whom his name had become a household word, and his departure was regarded by them in the light of a personal loss. For his services during the past year he received a clasp to his South African medal and nothing more. The Colonial Office made a strenuous but unsuccessful endeavour to procure for him a brevet-colonelcy, and made the following representation to the War Office in December 1879: ‘Until August 1878 Colonel Lanyon appears to have remained in the field, but Lieut.-Colonel Warren, though not occupying a higher position than that of Chief of Colonel Lanyon’s Staff, appears to have acted to a great extent independently and not under his immediate supervision; and when, at the close of the engagement of 18th June at the Paarde Kloof, Colonel Lanyon arrived with the Southern Column, he left Lieut.-Colonel Warren in command to complete the victory, considering that the entire credit of the brilliant success then attained was due to Lieut.-Colonel Warren. ‘In the operations at Kuruman and the capture of Litako and Takoon Lieut.-Colonel Warren not only behaved with dashing personal bravery as on previous occasions, but contributed materially to the success of an operation which in many particulars clearly resembled those just concluded against Morosi’s Mountain and Sekukuni’s Town.