Seeing the damage that can be caused by power being in the wrong hands, Nathan concludes that his father's idea of creating a super-powered army would be the best way to deal with it. Leaving Peter behind, he flies away to join Pinehearst. After taking over Pinehearst from his father, Tracy informs him of a project involving giving abilities to 50 Marines. However, he is foiled when Peter, assisted by Flint and Knox, destroy Mohinder's lab and research and burn Pinehearst down. After Peter injects himself with the formula in order to escape and save both of their lives, Nathan, disgusted with his brother, tells Peter he wouldn't have done the same for him, and leaves. Three weeks later, Nathan is talking with the President (portrayed by Michael Dorn) and convinces him that people with abilities need to be imprisoned. We later find out in the first episode of Fugitives, "A Clear and Present Danger", that Nathan has been appointed Chairman of Homeland Security by the President, giving him unlimited power to find and take his fellow evolved humans into captivity, whilst keeping the organization in the dark about his own ability. He plans to contain them and eventually find a cure for their abilities, but this is at odds to the aims of others working on the operation. Nathan hires Emile Danko, referred to as "The Hunter" by the fugitives, to work with Noah Bennett to try to capture the Heroes. Though Nathan's intentions with the Heroes are well-meaning, Danko sees differently. He wants to eliminate the people with abilities. This difference in perspective proves a strain in their working relationship, especially when Nathan orders Claire, his daughter, immunity. Despite allowing Peter to be targeted, Nathan tries to protect him as best as he can, risking everything to save Peter when he's shot by Danko and falls off a building. Nathan is aware that his plan is derailing in front of his eyes. He is finally able to fire Danko in "Shades of Gray" which leads The Hunter to confirm his theory about the senator having an ability; Danko pushes him out of a window and watches him fly away. At this point, Nathan, realizing Danko's next move, takes off for Costa Verde to pick up Claire. Though Nathan appears to be cold and calloused, he continues to show empathy for the fugitives. He repeatedly saves Peter, and tries to have a civil relationship with Tracy, whom he persuades to lie for him.