Transportation networks are canonical examples of complex engineered Systems of Systems (SoS). Despite the local correctness and independent governance of constituent systems such as traffic control infrastructure, navigation services, and public transit operations, transportation networks frequently exhibit large-scale behaviors that are unintended, difficult to predict, and not attributable to any single subsystem. This paper presents a detailed case study demonstrating how emergent behavior in transportation SoS can be systematically modeled, detected, and validated using Model-Based Systems Engineering (MBSE) and agent-based simulation. Three complementary scenarios are examined: a parallel freeway–arterial corridor, a signalized urban grid network, and a microscopic vehicle-level model reproducing phantom traffic jams. Emergent regimes are identified automatically using system-level metrics, enabling scenario-based verification and validation of SoS behavior. The results demonstrate that interaction structure—not component malfunction—is the primary driver of system-level emergence.