"We focus on research that has a high risk of failure, but if it succeeds, it makes a revolutionary difference in national security," said spokesman Jan Walker. "We spend a lot of time talking to the senior leadership to ask them, 'What are the things that keep you up at night?'"
DARPA is spending $15 million to use "megamaterials" developed by Duke University scientists to build shoot-through, invisible, one-way, self-healing shields for soldiers in urban battlefields. By bending light the wrong way, an optical trick can make objects disappear.
The agency created Stealth, Global Hawk, Predator and command and control systems that are being used today in Iraq. They also funded water purification systems and translation devices.
"We have a robust investment in urban warfare," said Walker. "We worried well before 9/11 about biological defense before the anthrax threats."
But Alexis Debat, senior fellow for national security and terrorism at the Nixon Center in Washington, D.C., told ABC News that many of these inventions have had "little value in the fight against terrorism."
"It's a very American thing to think that everything and anything can be solved by technology," said Debat, a consultant for ABC News. He said the military needs to focus more on human resources, recruiting more Arabic speakers and using old-fashioned police work in communities in Iraq and Afghanistan.
Military writer Weinberger agrees that weapons research is still dominated by projects more appropriate for the Cold War — like the F-22 aircraft.
"It's a really fine aircraft with some great technology, but not of much use for the war on terror," said Weinberger. "It was proposed at one point that it could help hunt down IEDs (improvised explosive devices). But the idea of using an aircraft that costs in the tens of millions of dollars to defeat a homemade bomb that costs a few hundred dollars is a bit absurd."
Much of the focus of the latest research is in neuroscience. Researchers at Stanford and Columbia universities are exploring the use of magnetic stimulation to keep soldiers in battle awake for days while preserving their cognitive function.
The military industrial complex, coined in the age of President Dwight Eisenhower, is alive and well today, according to Debat, whose research into how Muslims fight is partially funded by the Department of Defense.
"It's an unwritten rule in the U.S. economy that defense companies play an important role in the stock market as anchors of stability," he said.
"Living here in Washington, you have no idea how we are inventing enemies," said Debat. "Hundreds of people are trying to figure out how to make China our enemy because there is so much money and power in the Pentagon."
Still, "risky" research can offer advances that have ramifications far beyond the battlefield.
DARPA is funding research to create a prosthetics arm that can function like a real hand. The device gives sensory perception back to the fingers through nervous system signals.
Researchers at MIT are developing an artificial "exoskeleton" that will not only diagnose a soldier's injury, but treat it.
Drugs have been developed to enhance aerobic function without lung injury.
Global positioning systems, composite materials for aircraft and many medical advances owe the military for their entry into the civilian world.
"Much has carried over into the economy, so if you put it all together, it's worth it," said Kei Koizumi, research and development policy director at AAAS.
"The technology was built on years of earlier science and development," Weinberger said. "No one woke up one day and said, 'I'm going to build a stealth aircraft.' So when you ask: Do we take national security risks if we don't try crazy things, my answer is, 'No.' Should we try risky things? Absolutely."
"Let's let U.S. enemies do crazy things," she said. "And let's make sure the U.S. government does smart things."