When 11-year-old Altaaf is orphaned during a violent attack on his home by state police hunting a rebel leader, he is adopted by Inayat Khan, the kindly officer in charge of the raid, and his loving wife Neelima, whose son has just died in a freak accident. Altaaf's dream life with his new parents is shattered, however, when he discovers the man whom he now calls his father is also the task force leader who tragically gunned down his family.
Mission Kashmir follows the life and tragedy of a young boy named Altaaf after his entire family gets killed by police officers. Ironically he is adopted by the man who killed them. When Altaaf finds out, he seeks revenge. The movie deals with the India-Pakistan-conflict and especially with the tragedy of children suffering from war.