How about the US' first official national monument (not to mention the site of the film 'Close Encounters'), Devil's Tower?

http://www.nationalparklover.com/devilstower.htm

Or how about the Badlands? See the cult film classic 'Badlands' with VERY young Martin Sheen and Sissy Spacek for inspiration.

http://www.nps.gov/badl/exp/home.htm

Driving around anywhere in the area, you will stumble across the old Minuteman missile silo sites. Ellsworth Air Force Base was surrounded with 150 active silos. There were 1,000 of them around this area of the West at the height of the Cold War.

Dunno how 'Area 51' that is for your protagonist.

The great Paha Sapa, or Black Hills to English speakers, is full of sacred sites, and a huge draw for pilgrimmages for hundreds of thousands of people every year. But their main destination is often not, Mt. Rushmore, despite it being the most obvious to people from outside this area.

How about this for a pilgrimmage juxtaposition. There is the less visually spectacular, but still regularly used pilgrimmage site, Bear Butte State Park, in Sturgis, where Lakota sun dances still take place every year.

Bear Butte


Then, there is that other pilgrimmage to Sturgis, SD taken by nearly half a million people every year too, the Sturgis Motorcycle Rally. It is 63 years old this year.

Official Sturgis Rally site

Although I like the idea of Graceland, I think it has been terribly overdone, and is quite cliche.

Then, there is also the Wounded Knee pilgrimmage. The 1890 graveyard is across the highway from the burned out remains of the 1973 Wounded Knee occupation. There is a pilgrimmage every year, called the Wounded Knee Memorial. Kevin McKiernan was the only photographer inside the village during the takeover. His photos are here:

Wounded Knee takeover photos

BTW, don't think anyone has mentioned any caves. The Hills are home to one of the largest in the world. It is very mysterious:

Wind Cave

Wind Cave photos

Don't think you can learn more about the soul of America, than by making a pilgrimmage to the Black Hills.