The story mode consists of two episodes. The first episode is the same as the one found in the previous game, while the second episode is new. This second episode takes place after the "Subspace Incident" of the previous episode and deals with the swordswoman Nagisa and a new race of SEED infected humans called the Duman.
The gameplay features character support systems, allowing players to invite their created characters to join them in battle. New animations, weapons, clothing, and an increased level cap of 50 have also been added. The game includes a Rebirth system, which resets a character back to level 1 but gives points to increase a character's stats. There are new mission types, including Infinity Missions, Training Missions, and Open Missions with an additional Infinity ranked mission difficulty.
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