The first Armacham Technology Corporation employee encountered in F.E.A.R., Charles Habegger is already dead when the F.E.A.R. Point Man and Spencer Jankowski find him tied to a chair with his face partially cannibalized, eaten alive by Paxton Fettel, likely after being interrogated about the location of Alma Wade. Though dead, his voice is later heard in several phone messages throughout the game.
Before he died, Habegger recommended that the Perseus Project be suspended temporarily due to the likelihood of another Synchronicity Event following the reopening of the Vault. He later became angry when someone refused to listen to his advice, stating in another phone message that the last Synchronicity Event, which led to the Origin Project being permanently shut down, occurred when Fettel was only a child. Another Synchronicity Event, he said, would be much more catastrophic now that Fettel is an adult. Harlan Wade takes Habegger's side regarding the issue, stating to an unnamed ATC employee that Habegger thinks "people are blowing smoke up his ass" and that people should listen to the expert advice they're being given. Habegger also tries to convince Harlan that they needed to purge the Vault.
Through the Point Man's visions, it is revealed that Habegger was present at the birth of the project's first prototype. At the very beginning of the game, in a dream sequence, the Point Man hears a voice saying "I've tried to forget. I've tried so hard to forget." This voice is Charles's, speaking of the horror of Project Origin. Later, the Point Man sees his phantom image walk by a doorway and sees a flash of Charles's mutilated face in his mind's eye. Shortly after these events, the Point Man can also hear Charles say, "You were born here, in this place. I was there.", implying that Charles was Harlan's partner in Project Origin. Charles also asks, "Why did you bring me here? Why did you bring me back?" Fettel states that both he and Alma have memories of Habegger. This implies that Charles was actively involved in the project, but since both Fettel and Alma were exposed to him, Fettel does not know whose memories they actually are.
At the end of F.E.A.R. Extraction Point, the Point Man sees the bodies of the SFOD-D team lying on the roof of Auburn Memorial Hospital. If the Point Man looks carefully, he can see Charles Habegger lying on the ground.
- The scene in which Charles's ghost walks by a boarded up doorway in the Birthing Facility was originally supposed to show Alma instead, though this was changed at an unknown point.
- It is revealed through old in-game dialogue in the Director's Commentary video of the F.E.A.R. Platinum Collection that Marshall Disler was originally the dead man found in the Birthing Facility, although the model and dialogue are unchanged in the final game.