With the coming of the Suez Crisis and the heightened tension between Britain and Egypt that it brought, Johnston found himself expelled from the country 'virtually with the garments he was wearing'. He hoped to resume his pastoral duties in Egypt as soon as he was given permission to re-enter, but this authority never came. On resigning his See he was Vicar of Ewshot in the Diocese of Guildford until his death on 17 September 1963 after he collapsed preaching at a Battle of Arnhem commemoration service.