In the new region, the local language was Igbo, with a different culture of markets and farming. She was supported by the local missionary priests to introduce her and Sr Kavanagh to the local people. Their leprosy settlement was 4 miles from Abakaliki town with the only transport being by bicycle, despite this the leprosy service was successful. The first resident doctor was Dr Denis Freeman from Dublin. Dapsone tablets, an effective cure for leprosy, became the routine treatment by 1950. More medical services were being established in the diocese, when she returned from her first visit home to Ireland, Gogan was appointed the sister in charge at Ogoja as well as the regional superior at Obudu and the general and maternity hospital at Afikpo. Other sisters who joined the mission in Nigeria included Eileen Morris. In the following years, she was involved in the foundations of a number of general and maternity hospitals at Obudu, Ikom, Nkalagu and nDubia. She had been due to return home to Ireland for leave at the outbreak of the Nigerian civil war on 6 July 1967, but she chose to stay with her sisters until the battle front moved on from Ogoja diocese and the medical services were restored. She continued this work until 1969, when she was not physically fit enough to continue with missionary work.