This document describes the development of several tools for covert communication via network protocol modification. It begins with Timeshifter, which modifies the timing of ICMP packets at the network layer. Stegnet was then created to modify ICMP packet contents at the network layer. BitStegNet was finally developed to modify μTP packet headers within BitTorrent traffic at the transport layer, providing covert communication at a higher protocol level. The document outlines the implementation of each tool on virtual and physical test networks to successfully transmit hidden messages via timing or content modifications of network packets.