Perhaps we can't find consciousness in the brain because it is an illusion

... With the help of brain imaging, scientists can watch different parts of the brain light up, and they know they can alter the brain and our consciousness with surgeries or chemicals [sources: Eagleman, Pinker]. But what scientists don't know is at what stage of the process a firing neuron becomes a conscious thought. The things that make up consciousness may be scattered all over the brain, with different cranial parts responsible for different pieces of a person. But, as we've mentioned, there are tons of other brain mysteries about how these parts might work together.

Scientists are also trying to figure out the relationship between conscious and unconscious experiences. There are some things -- like breathing and maintaining a regular heart beat -- that we don't have to think about. How are these unconscious actions wired differently than the conscious ones? Is there any difference at all? We like to think we make our own decisions, but one recent study shows that we may not even do that. This study found that by using brain scanners, researchers could predict how a person was going to act a full seven seconds before the person knew that a decision had been made [source Keim]. Our consciousness might just be an illusion.

It's possible that something like free will could enter into the equation at the last possible moment, overriding the decision made by the brain. The researchers in the study also admitted that this test was best suited to a simple laboratory test that involved pushing a button, as opposed to a more important decision like taking a job [source: Keim].

via HowStuffWorks "Human Consciousness".