A level 5 atomic brain scan, also referred to as a phase 5 atomic scan, was a medical procedure relating to an organism's brain to detect any irregularities within it. When the clone trooper Tup was brought to Kamino for examination after suffering a mysterious mental breakdown, medical droid AZI-3 recommended a level 5 scan be performed to determine the source of the problem, as a level 2 scan failed to find anything. However, Chief Medical Scientist Nala Se refused, ostensibly on the grounds that Tup was too weak to survive the procedure.
ARC trooper Fives, desperate to save his friend, persuaded AZI-3 to carry out the procedure anyways, and the two located a tumor inside of Tup's brain that they removed. The tumor was actually Tup's decayed behavioral modification biochip, which had been implanted in all of the clones to ensure their compliance with carrying out Order 66. Tup died shortly after his chip was removed, and Fives later had AZI-3 remove his own chip in an attempt to prove their existence.