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 (VA: Kenichi Ono) - 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, after she attacks the Earth Cradle. In his first scenario, he's approached by the Gaiking team, but quickly leaves them behind.
Kusuha Mizuha (VA: Mikako Takahashi) - Female, pilot of the 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 the KoOhKi, piloted by a mysterious masked pilot, as well as the Mikene Empire. It is rescued by the combined efforts of the Mazinger and GaoGaiGar teams.
Brooklyn Luckfield (VA: Tomokazu Sugita) - 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 (VA: Kazuya Kaichi) - 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 antagonist group in the game. He is eventually captured by the Alpha Numbers, composed of the crews of the Albion (from Mobile Suit Gundam 0083: Stardust Memory) and the Argama (from Mobile Suit Z Gundam), and shown the evils of the Titans.
Seolla Schweizer (VA: Yumi Kakazu) - 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.
Ibis Douglas (VA: Akeno Watanabe) - Female, pilot of the Altairion and Hyperion. An inexperienced pilot, she is haunted by a crash that claimed the life of her mentor Filio Presty. When her scenario begins, she is rescued by the Crossbone Vanguard.
Tsugumi Takakura (VA: Tomoko Hasegawa) - Female, co-pilot of the Altarion and Hyperion. Playable only if Ibis is selected as the protagonist. Fiancée to Filio, she wears his glasses as a sign of remembrance.
Sleigh Presty (VA: Miki Nagasawa) - Female, pilot of the Vegalion and co-pilot of the Hyperion. Sister to Filio, she holds a deep, resenting grudge towards Ibis for accidentally killing her brother.
Other Original Characters
Viletta Vadim (VA: Atsuko Tanaka) - 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.
Rätsel Feinschmecker (Elzam von Branstein) (VA: Tetsu Inada) - Male, pilot of the Huckebein MK III L "Trombe". This is Rätsel's first appearance in the Alpha series, having previously appeared in Super Robot Taisen: Original Generation using his real identity.