UAV-enabled Integrated Sensing and Communication (ISAC) in sixth-generation (6G) wireless networks has sparked significant research interest. UAVs are positioned as aerial wireless platforms, extending coverage and improving Sensing and Communication (S&C) services. However, integrating UAVs introduces vulnerabilities due to multi-connectivity, necessitating robust security measures. To address this, efforts are focused on developing effective Intrusion Detection Systems (IDS). Here ML-based IDSs depend on the most suited Machine Learning (ML) algorithms for improved detection accuracy. However, inadequate detection features frequently contribute to the limitations of detection accuracy in various emerging cyber-attacks. Our study explores attack traits in UAV-enabled 6G networks, using complementary detection features to enhance ML-based attack detection. Additionally, existing Deep Neural Network (DNN) solutions for UAVs-enabled 6G networks mainly use single models (e.g., CNN, SVM, CGAN) instead of multi-tier models, (e.g., Hybrid, Fusion, Ensemble). Here, although the use of a single model can be faster for computer systems, it is difficult to understand the growing complexity of intrusion patterns in data. Also, these single models might not be good at recognizing the unique patterns of less common issues in datasets. Thus, we propose a fusion multi-tier DNN-based Collaborative Intrusion Detection and Prevention System (CIDPS) for critical UAV-enabled 6G networks. This system boosts accuracy without sacrificing latency reductions. Our approach learns decision boundaries from imbalanced data points using preceding DNNs sequentially. Moreover, most existing research works do not focus on intrusion prevention methods and deployment frameworks for UAV networks. This research proposes effective IPS mechanisms and deployment architecture for CIDPS in UAV-enabled 6G networks. It incorporates a CIDPS with an emergency response protocol, neutralizing attacks upon anomaly detection. We validate our solution through diverse dataset experiments (UAVIDS-2020, NF-UQ-NIDS-v2, 5G-NIDD). Unlike traditional practices where IDS are simulated, we implement CIDPS on actual UAV devices (PX4 Vision Dev Kit V1.5, DJI mini se, DJI mini 3 pro) and real-world UAV networks. Our approach outperforms prior algorithms with a 99.25% attack classification accuracy, higher detection efficiency, and lower resource usage, exceeding 99.05% detection rates.