In high-speed digital design, SI, PI, and EMI are not separate issues but a single physical phenomenon sharing Vias, PDN, coupling, and return paths. Based on WaveInSense webinar materials, this white paper organizes the causal chain of frequency domain analysis—from transmission line theory through Via Stub resonance, PDN anti-resonance, to a three-element model of system-level EMI. Finally, through an ultrasonic equipment EMC certification case study, it demonstrates how minimal changes targeting root cause structures led to certification acquisition and cost reduction (external chamber monthly usage reduced to 1/18 compared to the highest user).