The Three Shoguns arrived alongside the rest of the Descal Fleet to conquer Earth and were ordered by Captain Barder to collect the Cosmo Capsules. They fought alongside each other and served Barder loyally.
However, after the reveal of Barder as robot, the Shoguns' leader Blaird began to doubt their mission. Eventually, this would lead to Aqual accusing Blaird of disloyalty and kicking him out of the Three Shoguns.
After the destruction of Descal's flagship, the shoguns were saved by Garade and Grouza, who needed them alive to prevent any alterations to the timeline. However, their bullying and humiliation of the two shoguns eventually led to Aqual turning against them.
After King Neo Descal and Barreda arrive from the future, Aqual ends up defecting and teaming up with Sazer-X. Cyclead, however, is brainwashed by the two to be more aggressive. Upon being freed from his brainwashing, however, Cyclead joins Blaird and Aqual on the good guys' side, reuniting the Three Shoguns.