In the domain of digital data exchange, ensuring information security is the supreme demand for data storage and transmission. Interlinking cryptographic techniques with steganographic principles can enhance data confidentiality. However, there have been no reports thus far to develop molecular platforms for hybrid crypto-steganography systems. Using our synthesized nanoclusters (BSA-Au/Ag NCs) through bovine serum albumin (BSA) as a versatile scaffold, we fabricated a molecular platform for concatenated logic circuits and molecular keypad lock. Then, we integrate terrestrial direction information transmission through molecular navigation, employing a double block cipher by combining stego key and shifting cipher key techniques to develop a hybrid crypto-steganography system, aimed at enhancing security paradigms. Furthermore, we prioritize information protection by developing an enhanced distress call protocol using a polyalphabetic cipher to activate covert communication capabilities, thereby safeguarding data against potential infiltrators.