Michael Pollen explains the ego's "location" in the brain: It would be the default mode network, where much of your self-critical mind chatter happens. Taking psychedelics down-regulates this brain network.
Researchers describe the effect of psychedelics as "letting the brain off its leash", or firing the conductor to let the orchestra play. Without the default mode network acting as a dictator, areas of the brain that don't normally interact meet, producing phenomena like hallucinations and synesthesia.
An overactive ego may be what punishes those of us plagued with anxiety, addiction and mental health disorders. Psychedelics can have a beneficial effect by temporarily killing the ego, jogging the brain out of negative thinking patterns.
Pollen is the author of How to Change Your Mind: What the New Science of Psychedelics Teaches Us About Consciousness, Dying, Addiction, Depression, and Transcendence