In the distant future, humanity is hurtling down a path of ruin. Global environmental destruction caused by chemical contamination, radioactive fallout, and UV rays coming through the patchy ozone layer has lead to deterioration of the human genome.

As the War continues, Amuro and the White Base crew must make their way toward the Earth Federation Headquarters, Jaburo. On their way they meet several new enemies and face off against impossible odds. They fight in Operation Odessa to relieve the Earth from the clutches of the Zeon forces. Lives are lost, new friendships are made, and discoveries at every corner. Amuro soon learns that he possesses the powers of the mysterious Newtypes.

Cosplay City is in danger when the evil Dolmeck shows up. Commanding his army of monsters, he plans on destroying everything. Only one person can stop this: Cutey Honey. After she is released from her dormancy, Honey Kisaragi becomes the multi-transformational android Cutey Honey. However, the least is expected when Honey is faced with an old enemy from the past: Panther Zora.

Shikidouji, the illustrator of Shoji Gatoh's Full Metal Panic! light novel series, revealed that production has been green-lit on a "director's cut" version of the first Full Metal Panic!! television anime series from 2002. The director's cut will consist of three films. The announcement does not state if the film trilogy will add new footage.