 During the handover of power Dublin Castle he attended the blessing of the tricolour and had the honour of being the first to raise the flag officially at the ceremony, attended by Michael Collins.He supported the treaty and joined the Free State Army at the beginning of the Civil War rising to the rank of Major General of the Eastern Command.It was during this period that he came to public attention after the general manager of the Great Northern Railway Company, John Bagwell, was kidnapped by anti-treaty forces, on hearing of the kidnapping Hogan issued a proclamation to the effect that if he was not safely released, reprisals would be taken against anti-treaty prisoners in custody.