Context-sensitive smart defense represents a crucial element in protecting distributed cyber-physical systems against advanced and well-coordinated adversarial actions. The current defense architectures face serious issues, such as incompleteness of situational observability and a lack of cross-zone coordination during uncertainty conditions. In order to overcome these constraints, a context-aware smart defense system was proposed that integrates multi-source data and different learning approaches for Intrusion Detection System (IDS) and mitigation. The framework is a collection of data from a variety of sensors, surveillance cameras, radars, and threat databases scattered across numerous Defense Zones. During data transmission from multi-modality devices, there is a possibility of intrusion. For IDS, the network data is pre-processed using Deep Ladder Imputation Networks (DLIN) to fill in gaps and then dispersion-based normalization. Structured sensor and network data are used by the TabNet encoder, and cross-modal attention modules are used to preserve essential network features from different modalities. Graph Neural Networks are used to enable the spatial-temporal analysis to extract the contextual threat information. In the case of emerging or data-sparse zones, Auto Encoder-based Transfer-Learning (AE-TL) methods can be used to produce domain adaptation based on data-rich zones. When attacks are detected, a federated learning-based multi-agent reinforcement learning based on FedQMIX coordinates defense measures without violating data privacy. Bayesian threat inference is used to assess the possibility of future adversarial attacks in non-attack conditions. Empirical assessments indicate that the suggested transfer-learning approach achieves an accuracy of 98.50% and an F-beta of 97.85%. Federated learning combined with reinforcement learning attains an accuracy of 98.1% and 95.6% on attack data and generated data, respectively. Overall, the framework enhances threat detection and coordinated response capabilities, providing a solution to the protection of distributed cyber-physical infrastructures.