The breakpoint-based silicon debug approach allows users to stop the normal (system) operations of the circuits under debug (CUDs), extract the internal states of the CUDs for examination, and then resume the normal operations for further debugging. However, most previous work on this approach adopts the transaction-level or handshake-level of granularity, i.e., the CUDs can be stopped only when a transaction or a handshake operation is completed. The granulations at these levels are often too coarse when a transaction or a handshake operation requires a large number of cycles to complete. In this paper, we present a novel debug mechanism, called the Protocol Agency Mechanism (PAM), which allows the breakpoint-based debug technique to be applied at the cycle- level granularity. The PAM can deal with transaction invalidation as well as protocol violation that may occur when a system is stopped and resumed. Experimental results show that the area overhead of the PAM is quite small and the performance impact on the system is negligible.