Project Thebes otherwise known as "The Shady Plan"  is the project that has been slowly revealed over the course of the comic. Known conspirators of Project Thebes include Cain, Deimos, and Commanders Bering and Cook. Keeler is also a suspected co-conspirator, and Abel is a yet-unwitting participant.
Project Thebes is first hinted at during the closing of Chapter 1, where Bering asks Cain if he was successful, and Cain answers in the affirmative.
At the beginning of Chapter 2, Phobos warns Abel about Cain's recent string of navigators. Later, with the introduction of the character Deimos, and the revelation that he has been spying for Cain as well as passing messages from Bering and Cook (or perhaps spying on Bering and Cook for Cain), further suspicion is raised. Praxis is shown as having a hesitation to talk to Abel when he sees Deimos is nearby. This is later explained by a flashback in Chapter 4, showing that Deimos and Cain threatened Praxis if he didn't comply with Cain's demand: that no one touch, talk to, or look at his navigator.
|“||If our plan works, the boy's ability will emerge on its own. He'll fulfill his potential in ways he doesn't even realize are possible...||”|
During an argument at the beginning of Chapter 3, about Abel's volunteering himself and Cain to go on the mission to Colteron Space, Cain has a short flashback. It shows that the goal is to awaken some sort of special ability on the part of Cain's chosen navigator. It is implied that Cain realizes Abel is the navigator who has these abilities, and so he stops arguing with Abel and goes along with the mission.
The Heart of Project Thebes
|“||The device's song grows stronger. A swell of aggression... anger...||”|
Mid-Chapter 3, Mother is showing with some sort of device that is implied to be of Colteron origin. In the very next scene, Abel is shown to be studying a similar-looking device that is in a computer simulation of the Reliant's engine. When he tries to inspect it, an error message appears that says 'ACCESS DENIED'. Just then, Keeler appears out of nowhere and sends Abel to bed. Later, when the Reliant is on a collision course with a Colteron ship, this device activates after Abel expresses a desire to protect Cain. Instead of crashing into the debris from the enemy fighter, the Reliant disappears for a few moments and then reappears unscathed.
The next morning, Commander Bering reveals to Cain that Abel was successful in activating a secret jump drive, that is made from 'hybrid technology'. The theory is that the technology is activated by 'strong emotional desire'.