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In the year 179 of the New Western Calendar, the One Year War breaks out between the Earth Federation and the Principality of Zeon, but is halted when an object crashes to Earth, landing on South Atalia Island. An investigative team from the Extra-Over Technological Investigative Institute discovers the object is an alien battleship with highly-advanced technology. Despite the warnings of Dr. Bian Zoldark, the Federation hides the evidence of intelligent, extraterrestrial life, and uses the time to increase their military power. Bian founds the Divine Crusaders to utilize the Extra-Over Technology found on the ship to devise weapons capable of protecting the Earth from alien forces, should the planet become embroiled in a conflict.

During this time, economic troubles caused by the Federation's buildup sees the rise of many anti-Federation movements, such as the Neo-Zeon, who had retreated to the asteroid Axis. In response, the Federation establishes special forces units, such as the Titans and OZ. Other forces, such as the Demon Empire (from Brave Raideen) and Dr. Hell also threaten the Earth, but are pushed back by the teams of Mazinger Z, Getter Robo, and Raideen.

In the year 186, the Excelion battleship (from Gunbuster) battle a force of STMCs (Space Terrible Monster Crowd) when they are suddenly attacked by another alien fleet, known as the Aerogaters...

From this point on, the player can select from either a super robot or a real robot storyline, putting the player in command of the Grungust Type-2 or the Huckebein MK II, respectively.

Super Robot Wars Alpha allows the player to create their own character, giving them a name and birthdate, and selecting from 8 characters: four male and four female, The player then chooses another template and name for the character's significant other, as well as one of four personalities: "cool and nihilistic", "shy", "weird" or "hot-blooded", to apply a voice during combat. In the Super Robot Taisen: Original Generation series