There are three playable characters, however all three can use the same weapon sets, so there is no difference in gameplay (the exception is the costume "Katana Jaguar", which replaces on weapon in each set with a Katana. Which character you choose to play as makes no difference in terms of the story either since Bill and Jaguar are both in all of the cut scenes, even if during one player games.
- Bill is the original Contra, from the old NES game. After saving humanity several times from Red Falcon he eventually killed his partner and nearly destroyed the planet. He has been resurrected from cryogenic prison to eliminate Neo Contra, a new organization that poses a much greater threat to humanity than Bill ever did. Or so he's told...
- A mysterious alien sent to aid Bill on his mission. Despite being an alien in the forty-fifth century, he follows the code of the Samurai. He is the only character able to wield the Katana, the most powerful weapon in the game.
- A cybernetic soldier who served as Bill's partner and parole officer the last time Bill was revived, that time to destroy the Blood Falcons. They were the last threat humanity faced, as they were determined to wipe out the 20% of the world's population that wasn't killed during Bill's rampage.
The Contra Commanders
- The four commanders of Neo Contra and the bosses of the first four stages:
- This group answers only to Master Contra and have abilities and technologies superior to any of the foes you'll face getting to them. Only after killing them can you hope to challenge Master Contra.
- The leader of Neo Contra and threat to humanity. Aside from that not much is known about him. Before his amazing fast rise to power, nobody had ever heard about him. His true identity and plans remain unknown.
An old soldier who looks as if he has seen one two many battles. Less is known about his identity and plans that of Master Contra's; it can't even be determined if he is friend or foe. Regardless, the fact of the matter is he knows a lot about why Bill was brought back.
The alien who lead all of the early invasions of Earth several millennia ago is still around. He is being preserved by the Neo Contras for unknown reasons. Despite having very little of his body left, he is still a threat to the planet, especially in the hands of Master Contra.
This entity, while unknown to humanity, holds all of the answers about Neo Contra that Bill is looking for.