Sapkota became a central committee member of the Communist Party of Nepal (Maoist), led by Pushpa Kamal Dahal, in 1995, after the party split from the Communist Party of Nepal (Unity Centre). When the CPN (Maoist) decided to initiate an armed struggle, he went underground in 1996 and continuously led the movement. He led several party committees and commanded troops of the PLA during the 10-year-long people's war. He was elected politburo member from the party's second national conference held in February 2001. He was also elected a central member of the 41-member "United Revolutionary People's Council", a parallel state administration exercised by the Maoists, announced in November 2001. Sapkota, along with Krishna Bahadur Mahara and Top Bahadur Rayamajhi, were members of a dialogue team setup by the Maoists to hold peace talks with the government in 2001, which was unsuccessful in finding a middle ground after three rounds of meetings.