Modern computing systems rely on software defenses whose effectiveness ultimately depends on the integrity of the underlying processor hardware. Malicious hardware modifications, known as hardware trojans, can silently bypass these defenses and compromise the host system. Assessing their practical threat, however, requires looking beyond the malicious circuitry itself to consider operating-system behavior, hardware-software interactions, and constraints on attacker-controlled code execution. Adopting a systems-level perspective, this dissertation examines the practical operation of hardware trojans within general-purpose processors and subsequently explores their runtime detection through electromagnetic side-channel analysis. First, we introduce interrupt-resilient trigger mechanisms that enable dependable payload delivery despite non-deterministic operating-system interruptions, including context switching and multitasking. Second, we introduce a trigger mechanism that enables reliable trojan activation through runtime engines executing untrusted high-level code. This eliminates the need for attackers to possess prior arbitrary code execution, a restrictive assumption prevalent in prior work, and expands the practical threat surface to end-user devices. Finally, rather than attempting to detect trojans by isolating the minute electromagnetic emissions of their malicious circuitry, we investigate the anomalous microarchitectural activity induced by trojan-assisted software execution. We demonstrate a non-invasive, one-class classification approach that uses low-cost external sensing equipment to detect such activity at runtime, enabling hardware trojan detection on already-fabricated processors. Ultimately, the systems perspective reveals hardware trojans to be a system security problem rather than merely a circuit-level one, enabling more realistic threat assessment and new effective defenses.