In this chapter I describe and explain the judiciary’s increasing assertiveness towards military and civilian branches of government between 1999 and 2017. The chapter is divided into two sections. The first section discusses the trajectory of judicial–military relations during this period. It is divided into three phases: (1) 1999 to 2005, the early years of Musharraf’s rule when the judiciary remained cautious; (2) 2005 to 2008, when the judiciary and military clashed, leading to the fall of the military regime; and (3) 2008 to 2017, the period of constitutional democratic rule. In each period, I discuss the prevailing political situation, and the judiciary’s relationship with the military as demonstrated through its jurisprudence. Through this period, I show that the judiciary adopted a more assertive approach towards the military, beginning with contesting the military’s economic prerogatives, and gradually shifting to challenging the military’s political agenda and undermining the foundations of the regime, before seeking to take its place alongside the military as the overseer of Pakistan’s democratic political order.