She investigated agrarian history in the
Punjab. She argued that despite extensive irrigation works, colonialisation caused agricultural involution, with the number of workers per unit area rising and production dropping. She also analysed peasant movements in the erstwhile princely states of the Punjab across the pre- and post-1947 periods. Her critical analysis of a Marxian orientation of peasant consciousness has been highlighted. A common thread running through Mukherjee's work has been a criticism of the
Subaltern mode of historical inquiry, which informs her analysis of peasant movements as well as her other major contribution: modern Indian history. This is encapsulated by the two books co-written with
Bipan Chandra et al: ''India's Struggle for Independence
and India after independence: 1947-2000''. In the former book, the authors sought to "demolish the influence of the Cambridge and
Subaltern 'schools' reflected in the writing on colonialism and nationalism in India". ==Ideology==