Current network security technologies face new threats from determined attackers employing advanced evasion techniques such as IP spoofing, tiny fragment attacks, tunneling, and HTML smuggling. Conventional intrusion detection and prevention systems (IDS/IPS) have significant limitations in detecting zero-day attacks and sophisticated threats that can continuously alter their attack vectors. This paper presents a novel deep learning-driven, multilayer intrusion detection and prevention framework that integrates network-based IDS/IPS, host-based intrusion detection systems (HIDS), and honeypot technologies with advanced machine learning models, including graph neural networks (GNNs), autoencoders, and transformers. The framework employs adaptive learning mechanisms to enhance resilience against evasion techniques while maintaining low false positive rates. Experimental evaluation using diverse attack datasets demonstrates superior performance, achieving 97.3% detection accuracy for zero-day attacks and 94.8% resilience against advanced evasion techniques, significantly outperforming existing state-of-the-art solutions. The proposed framework contributes to cybersecurity research by introducing innovative multilayer correlation mechanisms, adaptive threat modeling, and evasion-resilient detection algorithms.