Before Scott went to France, he became involved with Córas Iompair Éireann (CIE) the National Transport Company which came into being on the 1 January 1945 as a result of the Transport Act of 8 December 1944. This was the last of a series of transport amalgamations as the independent bus companies and the railway companies had joined forces into two companies - Dublin United Tramways and Great Southern Railways. The new head of this transport firm was an accountant, A.P. Reynolds. Reynolds had built up a successful small bus company, The General Bus Company before the amalgamation and was friends with Sean Lemass (1899-1971) who was the Minister of Industry and Commerce in 1945. Reynolds was supposedly a moderniser but his tendencies were more towards modernising buildings than improving CIE's rolling stock and services. He was also a race horse owner and went racing with Michael Scott with whom he was also good friends. Scott was responsible for alterations to his house Abbeville, County Dublin, designed by James Gandon (1743-1823) and now owned by Lemass' son-in-law Charles Haughey (born 1925).

Scott had always made a point of cultivating those in power for commissions. In Ireland in the 1930s and 1940s there was little in the way of large architectural commissions that were not provided by either the Government or the Roman Catholic Church. Unlike the firm Robinson Keefe who cultivated the church hierarchy and educational institutions, and built a large number of churches and schools in the Dublin suburban area, Scott attached himself to Government ministers. He became very friendly with Sean Lemass who would later be Taoiseach between 1959 and 1966 and Scott's influence over the arts and architecture would be at its height at that time. In later years he was also very friendly with Charles Haughey, but Haughey was of a younger generation and friendly with Sam Stephenson (born 1933) and Arthur Gibney (born 1932) and so Scott's influence did not extend to his practice getting the best commissions of that period.

Also a member of this circle was the Jesuit Fr. Donal O'Sullivan who was later to become head of the Arts Council and also a friend of Scott. Scott had worked for the Jesuits at the behest of O'Sullivan. In later years this close relationship of Lemass, O'Sullivan and Scott was 'effectively state control of the arts'. So naturally enough, Scott got control of any CIE commissions that were going, being appointed Consultant Architect to CIE by Reynolds. Indeed at one time Reynolds wanted CIE to take over Scott's practice and have Scott and his team as in-house company architects, but Scott resisted, thinking of the political interference in projects and in the hiring of staff that would be incurred.

Scott generously passed on many of the commissions to promising architects, remaining as CIE's Consultant Architect. Scott's role as consultant architect meant that he passed all final drawings and designs for the various projects. These other projects included a large complex of railway workshops to be built at Inchicore (this was passed on to Eoghan Buckley and John OĠGorman but was never built due to CIE's financial problems) and the Bus Stations at Clonmel (completed by Eoghan Buckley, 1948) and Cork for which Scott sketched plans. A scheme for a large manufacturing works at Broadstone Station was passed on to Brendan O'Connor but was never executed due to a change in Government. However he kept the Dublin Bus Station and other key projects for his own practice.