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- Bren Turner - the main protagonist. He is originally from E.D.N. II, but is currently now a special transfer student at the NEVEC Advance Base on E.D.N. III. With a hot-blooded attitude, Bren aims to be number one.
- Gingira - an advanced prototype Vital Suit made by NEVEC. It houses a next-generation AI, giving it the ability to talk to its pilot when needed. Its "Master" Bren Turner was the one who gave it its name. It also holds the ability to make actions on its own.
- Julie Fliesher - a student at the NEVEC Tech Base on E.D.N. III. She is a bright mood maker who excels in the handling technique of her personal customized PTX Vital Suit.
- TeeKee - a priestess of the next generation bundling snow pirates "Takashi Mori pirates", which aims to co-exist with the indigenous biological Akrid that inhabit E.D.N. III, having been waiting for the awakening. She has a demure personality, but is always willing to participate in combat when needed.
- Chris Landbaird - a student at the NEVEC Tech Base on E.D.N. III. He is calm and reassuring, being among the elite members of the academy. His hand-to-hand combat skills and control of Vital Suits are top-notch. He also holds a fierce rivalry against new transfer student Bren Turner.
- Luan Forest - a senior student at the NEVEC Frontier Base on E.D.N. III. He is always seen with his device at hand, adding data to his already vast library.
E.X. Troopers tells of the fight between the snow pirates and the Akrid aliens on E.D.N. III. The game's protagonist is Bren Turner, a young man who's come to the academy (the game has a school theme) from E.D.N. II. There are also characters such as TeeKee, a female snow pirate who has the ability to communicate with the Akrid, and Gingira, a Vital Suit that's loaded with next-generation AI and can communicate with its pilot. Gingira calls Bren "Master."
The E.D.N. III planet has three bases, each with unique traits. Players select one of these to serve as their base of operations. The three bases figure into the story, as while Bren comes from one base, other members of the academy come from different bases. The story is told through "manga demo" cut scenes (similar to the PlayStation Vita game Gravity Rush).
- Using the code 729443 at one of the three NEVEC bases unlocks the Rathalos Armor from Monster Hunter for use with Bren.