In social networks, the discovery of community structures has received considerable attention as a fundamental problem in various network analysis tasks. However, due to privacy concerns or access restrictions, the network structure is often unknown, thereby rendering established community detection approaches ineffective without costly network topology acquisition. To tackle this challenge, we present META-CODE, a novel end-to-end solution for detecting overlapping communities in networks with unknown topology via exploratory learning aided by easy-to-collect node metadata. Specifically, META-CODE consists of three iterative steps in addition to the initial network inference step: 1) node-level community-affiliation embeddings based on graph neural networks (GNNs) trained by our new reconstruction loss, 2) network exploration via community affiliation-based node queries, and 3) network inference using an edge connectivity-based Siamese neural network model from the explored network. Through comprehensive evaluations using five real-world datasets, we demonstrate that META-CODE exhibits (a) its superiority over benchmark community detection methods, (b) empirical evaluations as well as theoretical findings to see the effectiveness of our node query, (c) the influence of each module, and (d) its computational efficiency.