Dark forces that threatened to destroy the world of La Gias have rescinded, if only for a brief. While the conflicts have been resolved, the Holy Kingdom of Langran is facing another war, this time with a new force: The Republic of Baronia. Forging an alliance with a long-time enemy of Langran, their goal is simple: to see the kingdom burn. In the midst of this new, twisted conflict, Masaki Andō and his team of Elemental Lords become independent from their previous masters, and form their own force to combat threats that can ravage the world of La Gias. Now, they venture out to find out what caused this new conflict to erupt.

After 16 years, the original Masou Kishin game finally receives a sequel. Like its predecessor and most of the games in the long-running Super Robot Wars/Taisen franchise, the game is a tactical RPG in a science-fantasy setting. Players control characters that pilot "Elemental Lords", robots with magical powers, powered by their pilot's prāna, or life force. The main objectives are to defeat enemies and progress through the story, often with branching paths that can impact the final outcome.

Once again, the terrain plays an important role in tactics. Terrain differences, as well as unit positions can impact the outcome of a battle. Units that attack other units from side or from back deal greater damage. While the combat system remains relatively unchanged, few elements were added from the main Super Robot Wars/Taisen franchise. For example, combined attacks to the enemy are now possible and they net both the main attacker and their partner experience points. Another one is the addition of assist attacks and defenses. If an allied unit possesses such skills, they can assist their friendly units when they are adjacent to them. However, their use is limited and so must be used wisely.