The side story takes place in 2017 a.t.b., between the rise of the “Black Knights” organization and the return of the supposedly "dead" Zero. The setting is in Europe, where the European Union (E.U.) allied nations are being invaded by the overwhelming forces of the Holy Britannian Empire. On the verge of defeat, the E.U. army forms a special unit known as “W-0″, of which a young pilot named Akito Hyuga is a member. Leila Malkal , a former Britannian Aristocrat comes to the E.U.'s aid, commanding the “Wyvern” Knightmare corps comprised of Japanese teenagers. They recklessly plunge into a battlefield, where the survival rate is extremely low, at about 5% only. They fight for their freedom and for a "home" to which they can return.
The Ark Fleet has been destroyed, and a significant number of the enemy's troops have been wiped out due to its crash landing. As the remaining forces of the Holy Order of Michael regroup in order to launch a final assault on Weiswolf Castle, the wZERO unit, along with their new ally Ashley Ashra, stand ready to intercept them. Meanwhile, with his Geass out of control, Shin moves to erase his younger brother's existence once and for all. But Akito, having promised Leila that he will come back alive, refuses to accept such a fate, and the two clash in their final battle.
Galo and the Burning Rescue Fire Department face off against BURNISH, a group of mutants who are able to control and wield flames, and the fire disaster they have unleashed on Earth.
In a quicksand surrounded town called Makka, rumors spread of a legendary robber named Gasback is after the town. To protect it, Mayor Kepler has hired bounty hunters. These hunters have been following Gasback from town to town in hopes of getting the bounty. Vash the Stampede is in town, along with Meryl and Milly, along with the female bounty hunter Amelia and Nicholas D. Wolfwood.
009 Re:Cyborg follows a group of nine cyborgs, each of them created by a shadowy organization for use as weapons against humanity. The group turns on their creators to protect the population instead, using the powers given them to fight their creators.