!!Nathan "Ladd" Spencer
* [[ArtificialLimbs Artificial Arm]]
* BadassMoustache: Grows a thick, American police chief-worthy manly moustache in ''Rearmed 2''.
* EmpoweredBadassNormal: In addition to his arm, Spencer has a number of [[RequiredSecondaryPowers secondary bionic improvements]] that, for example, provide armor, weaponize his adrenaline, allow him to jump superhuman heights and fall hundreds of feet without injury, and more. He looks mostly human, but he is far from it.
* SpellMyNameWithAnS: His nickname is sometimes spelled [[TotallyRadical "Rad Spencer"]].
** The official nickname is "RAD", and is explained as, when he originally lost his arm, he was the first person to be considered and tested on for bionic augmentation. He was therefore the most important part of the '''R'''esearch '''A'''nd '''D'''evelopment department for bionics. When he went into the field, he was humorously given the codename RAD from all his time in the labs.
* SuperDrowningSkills: Spencer's bionic arm is extremely heavy, and almost completely shuts down when exposed to water. Spencer therefore cannot swim in water as his arm drags him down.
* TookALevelInJerkass: Went from a typical cocky action hero in ''Rearmed'' to a brooding, "[[Webcomic/PennyArcade I smoulder with generic rage]]" anti-hero in the 2009 game.

!!Emily Spencer
* [[spoiler:DeadAllAlong- possibly as the process of creating the bionic arm has been never been explained so if she's truly dead isn't said]]
* DistressedDamsel

!!Super Joe
* [[spoiler:BigBad]]: [[spoiler:Of the sequel]].
* [[spoiler:BigBadFriend]]
* [[spoiler:FaceHeelTurn]]
* [[spoiler:TheManBehindTheMan]]
* MissionControl
* [[spoiler:RogueProtagonist]]
* [[spoiler: SuddenSequelHeelSyndrome: Besides his major role in the original ''Bionic Commando'', Joe was the player character in at least 3 other Capcom games back In the 1980's and 1990's. He then became the BigBad of the 2009 game.]]

!!Jayne Magdalene
* CutsceneBoss: In the Gardens, Joe goes into a boss arena with her and it looks like she's going to be a boss fight, but then he takes her out with one punch in a cutscene.
* FaceHeelTurn: A retroactive example; she's first seen as a Bioreign terrorist in the 2009 game, then in the prequel ''Rearmed 2'' we see her back in the day as an FSA soldier and ally of Spencer's.
* FauxActionGirl
* MoralMyopia: Considers civilians to be legitimate targets and their mass murder an act of "self-defense" because of the government's (admittedly pretty evil) treatment of Bionics in the Purge. She never reconsiders this, and only helps Spencer and turns against the Bioreign leader [[spoiler: Super Joe]] at the end because she felt he was just using her and the other Bionics as pawns.
* NotSoDifferent:
-->'''Spencer''': You're not a freedom fighter, you're just like me. A killer.
-->'''Mag''': Then [[StatingTheSimpleSolution why I haven't shot you yet]]?

!!Gottfried Groeder
* BigBad: [[spoiler:Subverted]]
* DragonAscendant: Went from Generalissimo Kilt's TheDragon in ''Rearmed'' to the co-leader of Bioreign in the 2009 game.