Mackney worked to improve the effectiveness and strength of NATFHE by seeking a merger of the trade union with the Association of University Teachers. Merger of the two unions occurred in 2006. Mackney was elected Joint general secretary along with AUT leader Sally Hunt. The new trade union represented about 120,000 academics and academic-related staff in further and higher education throughout the United Kingdom. Mackney suffered a severe heart attack in 2005. After an extensive recovery, he declined to run for the position of General Secretary of the UCU and retired from active union life. Mackney has been involved in larger trade union issues as well. In 1999, Trades Union Congress (TUC) general secretary John Monks appointed him to his first Task Group looking at the implications of the Stephen Lawrence report for trade unions. In September 2002, Mackney became the first NATFHE general secretary ever elected to the TUC General Council. Mackney became a founding member of a caucus on the TUC General Council known as "Fed Up With Losing." The caucus, which included Billy Hayes, Jeremy Dear, Mick Rix, Mark Serwotka, and Bob Crow among others, argued for a much more aggressive and militant labour movement which would push the Labour Party in a more leftist direction and begin to challenge the lingering effects of Thatcherism. The media began calling the group the Awkward Squad. Mackney is a lifelong opponent of racism and fascism. He has been involved in anti-racism activities since his youth. As a trade union leader, he pushed for establishment of the Commission for Black Staff in Further Education and has attacked discrimination against staff and faculty as well as societal racism which prevents students from obtaining jobs upon graduation. Mackney has also vocally opposed the British National Party and other organised and unorganised forms of fascism in British society. The offices of the Unite Against Fascism Campaign, backed by over 20 trade unions, were located in the NATFHE building in Britannia Street, Kings Cross. He is also a strong supporter of Palestinian independence. However, in 2006, Mackney opposed a NATFHE resolution supporting a boycott of Israeli institutions of higher education. Mackney was also an early and strong opponent of the Iraq War. He has spoken out angrily about British involvement in the war, and condemned the government for its continued involvement in the continuing military occupation of Iraq. The offices of the Stop the War Campaign, which organised the biggest British demonstration in labour history, were located in the NATFHE building in Britannia Street, Kings Cross.