Mr. Mukherjee took over the role of In-charge on December 25, 2021, which began amid the violence against Bharatiya Janata Party workers after the 2021 general elections, but TMC miscreants attacked him during the founding general meeting that was attacked in Sandeshkari. It faced difficulties early on as the party infiltrated the Bharatiya Janata Party office. Undeterred, he mobilized 50 local BJP volunteers to launch an FIR against the accusers and challenge the rule of local leaders Sheikh Shahjahan and Johar Sardar. Despite obstacles such as the demolition of the Duapara BJP party office in March, Mukherjee persisted as panchayat elections approached. The TMC orchestrated violence and intimidation to prevent BJP candidates from obtaining nomination papers, even laying siege to administrative centers such as BDO offices in Sandeshkari and Nazat.

In response, Mukherjee documented the TMC's misconduct, reported the incident to the authorities, and filed a petition in the High Court for a fair appointment process. The court ruled in favor of the BJP candidate and allowed his nomination at the safer SDO office in Basirhat Town. However, the candidates faced stiff resistance from the TMC, including violent attacks at the BDO office in Haroa and elsewhere. The Bharatiya Janata Party, led by Krishnendu Mukherjee, remained undaunted and persistent, with 80 candidates submitting their nominations at the Basirhat SDO office, achieving an important victory despite the difficulties. Mukherjee personally presented party symbols at both Sandeshkhali and Nazat BDO offices and navigated TMC-held areas despite risking his life.

Throughout the Sandeshkhali Movement, Krishnendu Mukherjee has remained steadfast in his support for the community, offering healthcare, financial assistance, and shelter. His resolute commitment and bravery have not only uplifted the villagers but also underscored the significance of grassroots movements in confronting political repression and promoting democratic principles.