Full Metal Panic? Fumoffu adapts content from novels 1 to 3, 5 and 6 of Shoji Gatoh's side story light novel series Full Metal Panic! Tanpenshuu. Episode 9 adapts content from the other side story series Full Metal Panic! Side Arms.
While listed as 12 episodes, Full Metal Panic? Fumoffu's original Japanese broadcast cut episode 2 due to current events regarding a series of kidnappings in Japan at that time. However, this episode is included in the DVD version.