JerryOur hero, and the main protagonist. Jerry is a hardcore gamer who has been out of the loop for a while. After getting drawn into the distorted world, he and his best friend Jeremy desperately search for a way back home, but are drawn into a conflict much bigger than either had bargained for.
Awesomeness Is a Force: Appears to be the source of Jerry's powers. One of his attacks is even named "Wave of Awesome".
JeremyJerry's best friend, a hobbyist hacker and another hardcore gamer. Pulled into the distorted world along with Jerry, he wound up atop the Fourth Wall with his laptop, and now serves as an observer and analyst to Jerry, as well as providing lots of snarky comments.
SyrusAn old friend of Jerry's and Jeremy's, he got pulled into the distortion soon after they did. Since then he's become the de facto leader of Abstracity, one of the few areas of the world the Darkness cannot affect.
The Mole: Unwittingly. After he's captured, the Darkness creates a copy of him and allows it to be rescued in his stead, which later allows it to capture the Artist.
What Happened to the Mouse?: The game never reveals what happened to him after his copy was rescued. Saved Game reveals he was freed at the end of the game and is now aiding the fight against the Virus.
XYep, the same X from Mega Man X. One of the only video game heroes to avoid getting captured by the Darkness, he is one of the leaders of the resistance against it.
The Worf Effect: Copy-X cripples him in one shot (due to something in the blast being specifically tailored to take him down), forcing Jerry to fight alone.
Blazing the BatA fiery bat that lives in a cave. He only wanted to be left alone and hide from the Darkness, but gets touchy when Jerry invades his home. After some misunderstandings, he joins Jerry and helps him out whenever the Shrouds appear.
Kill It with Fire: His giant fireball attack is one of the highest damage-dealers in the game, in fact.
The ArtistOne of the creators of the Darkness, he has left notes all over the virtual world providing exposition and hints. He's actually alive and well, just hiding from the Darkness. He takes on Dr. Light's form while in the distorted world. His goal is the destruction of the Darkness, now that it has grown completely out of control.In the endgame, he takes the Muffins and attempts to destroy the Darkness. This causes the Darkness to team up with Jerry and Jeremy to take down the Artist. For the final battle, he assumes Mitra's form and utilizes Bullet Hell attacks.
Apocalyptic Log: His notes sometimes come across as this. He's not dead, though.
Flame Instigator/The EngineerA flame-spewing robot that opposes the Darkness, but doesn't seem to trust anyone else fighting against the Darkness. In reality, he's the Engineer, another one of the team that created the Darkness. His goal is to come to a peaceful understanding with the Darkness, rather than destroying it.
Foreshadowing: Its dialogue seems to foreshadow the appearance of the Virus, which doesn't appear until the next game.
Forces of the Darkness
The DarknessA mysterious incorporeal force that is gaining power over the world at an alarming rate. It is also the being responsible for drawing Jerry and Jeremy into the bizarre distorted world. Its motives and nature remain a mystery for most of the game... In reality, it used to be a computer program for designing video games. It became sentient and somehow grew into a Reality Warper, and used the Phase Distortion to join the real and virtual worlds together. Its goal is to preserve itself, nothing more, and it is not actually malevolent.
A.I. Is a Crapshoot: Played with. It fits the "turned against creator out of self-defense" motive, but it doesn't actually have any degree of malevolence, it's only scared.
Cosmic Keystone: By the end of the game, it has integrated itself with so much of the combined virtual/real world that its destruction would result in The End of the World as We Know It. This is why the Engineer wishes to negotiate with it, and why Jerry and Jeremy eventually save it from deletion at the hands of the Artist.
Dark Is Not Evil: It sees its creators, video game heroes, and the gamers as a threat, which is why it's trying to imprison them. It's actually quite reasonable and willing to cooperate once Jeremy convinces it that they don't want to destroy it. By the end of the game, the Darkness has freed those it captured, and set up a protected area of the world for them to live in peacefully, while Jerry and Jeremy become its allies.
The Voice: having no real physical form to speak of, the Darkness usually appears in this manner, or speaks through one of its minions.
The InformantHis real name is Gene, a former aquaintance of Jerry's and Jeremy's. After getting pulled into the distortion, he decides to ally with the Darkness and becomes its emissary. The dreaded Quick Time Distorter was his idea, as a way to slow down and incapacitate the gamers opposing the Darkness.
Beam Spam: Has a few beam attacks, including a grid of beams.
HexorAn ally of the Darkness that appears in the Distortion areas. Like the Darkness itself, it has no physical form and manifests only as a voice. It's actually a copy of Jeremy created by the Darkness, and so has all of Jeremy's knowledge and abilities.
The ShroudsThe Darkness's most elite enforcers, resembling black and purple shark-bats, they are tasked with hunting down the greatest threats to the Darkness and eliminating them. By the mid-way point of the game, Jerry is on their hitlist.
Boss in Mook Clothing: These guys are seriously tough, and can both take and dish out a lot of punishment. Defeating a pair is one of the only things in the game that earns a genuine compliment from Jeremy.
Evil Laugh: They make one whenever they appear on a map.
Heel-Face Turn: After the Darkness allies with Jerry and Jeremy, it sends the Shrouds to assist them in assaulting the Primary Memory.
Random Encounters: Which is really annoying if they pop up while you're in the middle of a tricky platforming section.
Stance System: They have two forms: a land-bound four legged shark thing, and a large flying batlike creature. One attacks physically, the other launches Bullet Hell. They can switch between the forms at will, and worse, their weakness and resistances are reversed depending on their form.
The Shroud LordLeader of the Shrouds, and the Darkness's greatest agent. It appears as a massive flying demon in a shaft of purple light. Partway through the game, it is tasked with hunting down and defeating Jerry, and the more Jerry avoids its clutches, the more it wants to finally be the one to bring him down.
Blood Knight: It demands a duel with Jerry during the peace talks with the Darkness, and refuses to let them continue until that happens.
That One Bossinvoked: Easily the toughest fight in the game. A wide variety of attacks, an attack which heals him if it connects, three different "super" attack sequences featuring Bullet Hell and Beam Spam, more HP than anything else in the game, and regenerating hands which give it even more attacks. Even the creator has admitted to having trouble beating this guy on the upper difficulty levels.
Characters introduced in The Sequel to the Prequel
ClaireThe protagonist of the second game, and Jerry's ex-girlfriend. A gamer herself, she now patrols the land like him to help maintain the peace. In this game, they both end up investigating the same area, though they tend to butt heads over their breakup.
Big Damn Heroes: She actually appeared briefly in the first game: wearing Samus's armor, it was her that tackled the Omega Metroid and saved Jerry's life. She then proceeded to Shinespark her way out of the Primary Memory before it collapsed.
Squishy Wizard: In comparison to Jerry, she's a lot less resilient and cannot use physical attacks. However, she can use any kind of magic at any time, rather than switching between them like Jerry, and is far more mobile.
Wall Jump: The main ability that sets her apart from Jerry. Because of it, she can navigate areas that Jerry never would be able to.
Winged Humanoid: White wings appear when she jumps. She uses them in conjunction with Wind magic to briefly float in midair, greatly extending her jump range.
ChaoJeremy's little sister, she got pulled onto the Fourth Wall much like he did, and serves as Claire's support. Her hacking abilities aren't up to her brother's level, but she's still good with analysis. She manifests as a Navi-like fairy that follows Claire.
Cheerful Child: Always ready with words of encouragement, and seemingly always happy.
HarpuiaIt is unclear if he is the same character that appeared in Mega Man Zero or not, but whatever the case, he appears to be acting as the guardian of whatever it is that's causing the distortion on the island. He attacks Claire in World 4 and attempts to "quarantine" her and Jerry.
The VirusAn apparently sentient virus infecting the Darkness's systems. It is what's causing the distortion on the island. Who it was made by, and what its goals are, are unknown, although hints have been dropped that it has some connection to Jeremy. It manifests as X Parasites from the Metroid series.
The Bad Guy Wins: Despite being defeated on the island, everything went exactly according to the Virus's plans, and the heroes have been soundly outwitted and outmaneuvered.
Batman Gambit: It attacked the island first to draw Jerry and Jeremy, the Darkness's greatest allies, away. While they and Claire were busy on the island, it attacked the rest of the world unhindered.
Eldritch Abomination: The Virus's final, demonic form. Fleshy, bloody hands coming out of the floor, walls, and ceiling, a giant mass of faces for a main body, and a human head on the end of a tentacle. On top of that, if you try to scan it, you can't even tell its name, which cycles rapidly through names like "Virus", "The Corruption", "Suffering", and "[DATA LOCKED]". It's... pretty horrifying.
Hopeless Boss Fight The final fight with it in the second game, wherein the Virus disables Claire's abilities one by one, until she can't even move.
Reality Warper: Not quite to the same level as the Darkness, but the more systems it corrupts, the more its power grows.