Gundam F90 begins with the Jupiter Energy Fleet Supply Ship Kobayashi Maru returning from Jupiter to the Earth Sphere. The ships operator soon detects an abnormal spread of Minovsky Particles in the area. Immediately soon after the Kobayashi Maru is sunk by an unknown enemy and flash forwards three days to a test piloting of the new Gundam F90 mobile suit.

During testing of the F90, One of several people abord the Admiral Tianem (Named after the famous Earth Federation general who led the final assault on Zeon in the One Year War in Operation Star One) a Clop class ship, which the F90 is attached to, Lieutenant Rosch, the man in charge of the test team, comments that he is impressed with the SNRI’s (Strategic Naval Research Institute, the group that designed the Formula series of Mobile Suits) idea of scaling down mobile suits to enhance performance while minimizing target space and getting rid of useless armor that would not protect the unit in the age of beam weaponry. He is also impressed that the Formula series is still highly maneuverable despite the smaller size and reduced number of thrusters. An engineer says that SNRI hopes to return mobile suits to their original purpose of construction and to eliminate the use of them as weapons of war.