UFOs, extraterrestrial encounters, baffling disappearances-Mysteries Uncovered investigates, without prejudice, some of the most notorious, disturbing, and enduring mysteries ever recorded.

- UFO activity: the Roswell Incident, the Phoenix Lights, the Rendlesham Incident...
- Alien abduction: the Barney and Betty Hill case...
- Uncanny events: the missing crew of the Marie Celeste, the lost colony of Roanoke, the fate of Amelia Earhart...
- Notorious disappearances: the cases of Lord Lucan and D.B. Cooper...

For every instance rationalized away, there is another that defies explanation...