Following his transformation from being Jordan Shepherd, Daedalus is kept in holding at the US Military compound based in Iceland. However, when the Chimera attack, Richard Blake attempts to kill Daedalus, but only helps him to escape. Just prior to this, Daedalus speaks to Nathan Hale using telepathy and says: "They are calling to us. Can you hear them? It is beautiful".
Following his escape from SRPA Station Igloo, Daedalus assumes the position of Commander within the Chimeran forces and renders Angels obsolete. He continues to appear throughout the game, most notably in Bryce Canyon and in the Holar Tower, where he manages to kill Benjamin Warner and Aaron Hawthorne and severely injures Nathan Hale as well.
The Chicxulub Crater
Hale manages to finally confront Daedalus on board the Chimeran mother ship, when it's flying above the Chicxulub Crater. Prior to their final fight, Daedalus informs Hale of his disappointment, as he can't understand why he is still fighting for the Human race when they turned their back on him.
Hale ignores his mind games and defeats Daedalus.