Following the success of the original Crimson Sea, KOEI returns to the Theophilus galaxy, two years later, for the setting of Crimson Sea 2. After a surprise attack was executed by the mysterious, evil, alien threat from the original game, the IAG was left in a state of near collapse. Commander Live-D, leader of the IAG agency whose duty is to protect the galaxy, organizes all remaining forces, along with a roughneck group of mercenaries and survivors.
Sho, who is of a rare human-alien hybrid species known as "Vipa," finds that his old friends from the G-Squad have been dispersed to different areas of the galaxy. Faced with the devastation from the surprise attack, Sho sets out to look for additional help in battling the alien threat thought to have been defeated two years earlier.
Crimson Sea 2 includes over 60 missions; more than double the original Crimson Sea's 24. Also new are the game's "secondary missions," in which players can build up the power and weapons of their character and become better prepared to complete objectives that are initially too difficult. Character-specific missions, and the ability to switch between Sho and Feanay (a new and playable character) can be obtained once certain conditions are fulfilled. Two new gameplay modes, Co-Op and Versus, round out the key features in Crimson Sea 2.