Molecular Communication is evolving as a supradiscipline of bioinspired information and communication technologies. The next breakthroughs in molecular communication will greatly depend on the deep understanding of complex diseases, epitomized by brain malignancies. This will be achieved by delineating underlying cellular and sub-cellular processes in the context of interactive bionanomachines and their comprehensive management with diagnostic and therapeutic interventions controlled externally. In this paper, we present our recent progress in the fields of Externally Controllable Molecular Communication and brain malignancies, aiming towards drastic transformation in the way we diagnose and treat such disorders. Promising recent data involve targeting cell- and exosome-mediated theranostic systems as well as phenotypic switching and network formation. With the aim to transform Externally Controllable Molecular Communication from a theoretical concept to a clinically applicable technology, we identify gaps and challenges and share our views and thoughts on how advancements in diagnostics and therapeutics based on bionanomachine, nanonetwork and bionanodevice interfaces can bring a paradigm shift in the way we manage malignant disorders, via targeted breakthroughs.