Sparse events, such as malign attacks in real-time network traffic, have caused big organisations an immense hike in revenue loss. This is due to the excessive growth of the network and its exposure to a plethora of people. The standard methods used to detect intrusions are not promising and have significant failure to identify new malware. Moreover, the challenges in handling high volume data with sparsity, high false positives, fewer detection rates in minor class, training time and feature engineering of the dimensionality of data has promoted deep learning to take over the task with less time and great results. The existing system needs improvement in solving real-time network traffic issues along with feature engineering. Our proposed work overcomes these challenges by giving promising results using deep-stacked autoencoders in two stages. The two-stage deep learning combines with shallow learning using the random forest for classification in the second stage. This made the model get well with the latest Canadian Institute for Cybersecurity - Intrusion Detection System 2017 (CICIDS-2017) dataset. Zero false positives with admirable detection accuracy were achieved.