The Socialist Labour Party held a majority on the committee and disagreed, at one point having MacDougall and Peter Petroff removed from a meeting for trying to debate the subject. Opposing the war often led to trouble from the authorities and confrontations with pro-war groups. In 1916, he and Jimmy Maxton spoke at a meeting on Glasgow Green against the deportation of David Kirkwood, and the two were arrested and charged with inducing workers to obstruct the war effort. They were advised to plead guilty, and were sentenced to twelve months; around the same time, Maclean, Willie Gallacher and many other leaders of the Clyde Workers' Committee were jailed. Kept in Calton Jail in Edinburgh, MacDougall struggled mentally during his time inside. At the 1918 general election, MacDougall stood for the BSP in Glasgow Tradeston. Unlike some BSP candidates, he did not receive the support of the Labour Party, although its local Glasgow committee gave him its support, so he did not face any Labour opposition. He took 19.4% of the votes cast, the best performance of any BSP candidate who did not have official Labour Party backing. Unconvinced about the merits of the new Communist Party of Great Britain (CPGB), Maclean established the Communist Labour Party in 1920, but was not able to attend the founding conference, so MacDougall led support for Maclean's positions at its founding conference. However, Gallacher convinced a majority of delegates that it should instead seek to join the CPGB, barracking the official speakers and nearly starting fights, and he succeeded in defeating MacDougall in the votes. Maclean left the group, joining the Socialist Labour Party, and MacDougall may have followed him. In 1919, a Scottish Labour College was opened, largely on the initiative of Maclean, MacDougall, Maxton, Gallacher and Helen Crawfurd. Two years later, the offices of the Scottish Labour College were raided by the police, and MacDougall was sentenced to sixty days in prison for incitement and sedition. This second imprisonment led MacDougall to suffer what was described as a "nervous collapse", and kept him out of political activity for some time. As he recovered, he spent time trying to organise unemployed workers as part of Maclean's Tramp Trust Unlimited and did some work at the Scottish Labour College, but became increasingly disillusioned and gave few speeches. The CPGB unsuccessfully attempted to persuade him to resume political activity for them; however, he wrote a number of articles for "Communist Review" in 1925 and 1926 and appears to have briefly held membership of the party.