HAARP's purpose is to study the ionosphere (the section of the atmosphere beginning about 50 miles up in which ultraviolet radiation temporarily strips atoms of their electrons), the magnetosphere (the region in space above the ionosphere where the Earth's magnetic field affects the behavior of charged particles) and the Van Allen radiation belts (bands of highly charged particles contained in the magnetosphere beginning some 400 miles up). Scientists are interested in the ionosphere because of its ability to affect radio signals; the Van Allen belt, because the radiation there damages satellites, and a better understanding of it could lead to ways to make satellites last longer. "It's an open plasma-physics laboratory," says Dennis Papadopoulos, a physics professor at the University of Maryland who helped conceive the idea for HAARP with the Naval Research Lab more than 30 years ago. "You test ideas and scientific theories. Then, if something's important to the Department of Defense, you apply it."
I don't think we have been informed about the true nature of HARP. Not in this article and certainly not in conspiracy theories. It's probably for something secret, but rather benign. Like communication with submarines while they are submerged. Perhaps a radar system that can detect stealth aircraft. I don't think it matters, I'm not loosing any sleep worrying about it, whatever the truth may be.