Crimson Sea takes place in the vast system of Theophilus. Players set off on the journey of a lifetime, battling strange creatures in order to uncover the truth and realize their destiny. You play as Sho, a brave young man with a clouded past, and join him as he gathers a group of highly individualistic teammates to battle strange enemies in a number of unique missions.

With non-linear game progression and over 60 different missions, players can choose from among several missions created for each stage. Players may be asked to penetrate an enemy stronghold and gather intelligence, or rescue a stranded dignitary. Even after declining a mission, the player can still develop a character's attributes and weapons while exploring a stage. This allows the player to later accept a mission that was previously too difficult to complete.

Along with a variety of new weapons and effects, CRIMSON SEA 2 also features a series of enhanced Neo-Psionic attacks- deadly energy waves that change the tide of battle in a single move. By combining various weapons and Neo-Psionic techniques, a player can attack hundreds of enemies in a minute and achieve a thousand hit combos.