This paper presents a game theoretic model that analyzes resource allocation strategies against an adaptive adversary to secure cargo container transportation. The defender allocates security resources that could interdict an unauthorized weapon insertion inside a container. The attacker observes the defender's security strategy and chooses a site to insert the weapon. The attacker's goal is to maximize the probability that the weapon reaches its target. The basic model includes a single container route. The results in the basic model suggest that in equilibrium the defender should maintain an equal level of physical security at each site on the cargo container's route. Furthermore, the equilibrium levels of resources to interdict the weapon overseas increase as a function of the attacker's capability to detonate the weapon remotely at a domestic seaport. Investment in domestic seaport security is highly sensitive to the attacker's remote detonation capability as well. The general model that includes multiple container routes suggests that there is a trade-off between the security of foreign seaports and the physical security of sites including container transfer facilities, container yards, warehouses and truck rest areas. The defender has the flexibility to shift resources between non-intrusive inspections at foreign seaports and physical security of other sites on the container route. The equilibrium is also sensitive to the cost effectiveness of security investments.