Prometheus is originally thought of to be an enemy of Michael Ford and a threat to the country. It was believed that he betrayed The Trust and now were turning its members against the organization. This is proved to be wrong after the battle at Jefferson's Memorial when Prometheus saves you from the drudge forces. From that point on Prometheus and Michael Ford work together to combat the drudge forces and try and bring down Mr. John Adams and the Trust.
As you progress through the game you learn that Prometheus was one of the first of The Drudge to land on Earth and he was captured by the Trust and used as a template to create more drudge. These new drudge are controlled by Adams in his secret plan to take over the United States. To avoid being used to create more drudge, Prometheus leads Michael to where he is being held and tell him to set his pod to self destruct. Prometheus's body is then destroyed though he uploads his consciousness into the All Seeing Eye so he can continue to communicate with Michael and help him in the fight against Adams and his army of Drudge.
Prometheus could also have some mythological meaning as well. In Greek Mythology, there is a titan named Prometheus. Prometheus had betrayed the titans by giving the gift of fire to humans, and so he had been chained to a rock with an eagle picking at his body for all of eternity. This can be related to The Conduit's Prometheus: Prometheus gave some Trust operatives (the ones seen in mission 2) as well as Michael Ford the knowledge and ability to fight back against Adams, which is similar to giving humans the knowledge to create fire. Prometheus being held in a containment chamber while having DNA extracted from him is similar to being chained to a rock with an eagle picking at him. To further evidence this claim, in mission 7, there is a short segment before you face the first Invader when you travel through a wrecked building. On the floor in that building, there is a painting of Prometheus from greek mythology chained to a rock with an eagle. This further suggests that there is an intensional mythology connection between Prometheus and Prometheus.