This season is a direct continuation of the Zero Duel Masters with the same alternative setting, plot and characters. The only difference between both season were the shift from 2D to 3DCGI animation.

It follows after the duel of Shobu vs. Hakuoh, later unveiling Hakuoh and Jura were cooperating with the series' main antagonist: Professor March, who aims to control every creature by obtaining every Duel Orb.

(Source: Duel Masters Wikia)