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When starting the game, the player chooses between four scenarios, one for each combination of a male or female protagonist and super or real robot, as follows:
Super Robot Pilots
Sanger Zonvolt - Male, pilot of Grungust Type-3 and the Dynamic General Guardian, "DyGenGuard". He first appeared in Alpha Gaiden. Sangar awakens to battle a mysterious female who wants him dead, after she attacks the Earth Cradle. In his first scenerio, he's approached by the Gaiking team, but quickly leaves them behind.
Kusuha Mizuha - Female, pilot of Ryujinki and RyuKoOh. This is Kusuha's second appearance in the Alpha series, and is the only returning selectable character from Alpha. At the start of her story, the RyuOhKi reappears, attacked by KoOhKi, piloted by a mysterious masked pilot, as well as the Mikene Empire. It is rescued by the combined efforts of the Mazinger Z, Venus A, Boss Borot, Volfogg and "Cyborg" Guy Shishioh.
Brooklyn Luckfield - Male, alias "Bullet", pilot of the KoRyuOh. This is Bullet's second appearance in the Alpha series, and is playable only if Kusuha is selected as the protagonist.
Real Robot Pilots
Arado Balanga - Male, pilot of the Huckebein MK III and the Wild Wurger. He is one of two characters to begin as a member of the Titans, an antagonistic group in the game. He is eventually captured by the Alpha Numbers, comprised of the crews of the Albion (Gundam 0083) and the Argama (Zeta Gundam), and shown the evils of the Titans.
Seolla Schweizer - Female, pilot of the Wild Falken. Playable only if Arado is selected as the protagonist. She is the second character to begin as a member of the Titans.
Tsugumi Takakura - Female, co-pilot of the Altarion and Hyperion. Playable only if Ibis is selected as the protagonist. Fiancée to Filio Presty, she wears his glasses as a sign of remembrance.
Sleigh Presty - Female, pilot of the Vegalion and co-pilot of the Hyperion. Sister to Filio Presty, she holds a deep, resenting grudge towards Ibis for accidentally killing her brother.
Other Original Characters
Viletta Vadim - Female, pilot of the Huckebein MK III R (regardless if Arado is the protagonist or not). This is Viletta's second appearance in the Alpha series, and is the only active member of the SRX Team.
The first Super Robot Wars that uses the "Squad System", which allows the player to arrange squads (up to 4 units) to participate in battles.
The first game to introduce "Dynamic Kills", variants on attack animations, such as Daitarn 3's Sun Attack (which, incidentally, has been used since some of Daitarn 3's earliest appearances), that show certain attacks destroying targeted enemies, whereas most attacks would proceed exactly the same, regardless of whether they destroyed the enemy or not. Some attacks, such as GaoGaiGar's Goldion Hammer, had special variants for specific enemy types.
