The game was developed aimed for new players that may not be familiar with other series. For that reason, Banpresto Original characters that appeared as guests in previous games are the main characters in this game, and characters from other series appear as guest characters. The game also includes an optional tutorial where Masaki teaches basic commands. The tutorial can't be accessed after unlocking Shu's scenario in the Super Famicom version, but it is always available in the PlayStation version.
The game contains three scenarios, each with a different difficulty. The three scenarios interact with each other, with the progress and choices made in one scenario affecting story branching and units obtained in other scenarios.
This is the first game in the series to allow players to upgrade weapons.
After the war against the Divine Crusaders in 3rd Super Robot Wars, many robots and their pilots began to disappear. When Masaki Andoh returns to "Ragias Kingdom", his homeland. However, he is shocked to find that the main goverment from his kingdom was eradicated by terrorists.