Botnets are computer networks controlled by malicious actors that present significant cybersecurity challenges. They autonomously infect, propagate, and coordinate to conduct cybercrimes, necessitating robust detection methods. This research addresses the sophisticated adversarial manipulations posed by attackers, aiming to undermine machine learning-based botnet detection systems. We introduce a flow-based detection approach, leveraging machine learning and deep learning algorithms trained on the ISCX and ISOT datasets. The detection algorithms are optimized using the Genetic Algorithm and Particle Swarm Optimization to obtain a baseline detection method. The Carlini & Wagner (C&W) attack and Generative Adversarial Network (GAN) generate deceptive data with subtle perturbations, targeting each feature used for classification while preserving their semantic and syntactic relationships, which ensures that the adversarial samples retain meaningfulness and realism. An in-depth analysis of the required L2 distance from the original sample for the malware sample to misclassify is performed across various iteration checkpoints, showing different levels of misclassification at different L2 distances of the Pertrub sample from the original sample. Our work delves into the vulnerability of various models, examining the transferability of adversarial examples from a Neural Network surrogate model to Tree-based algorithms. Subsequently, models that initially misclassified the perturbed samples are retrained, enhancing their resilience and detection capabilities. In the final phase, a conformal prediction layer is integrated, significantly rejecting incorrect predictions, of 58.20 % in the ISCX dataset and 98.94 % in the ISOT dataset.