The game takes place three years after the events of Game Freak: Legend of the Sea, and Jake meets the new identities of his friends and partners, and new secrets of "The Game" are revealed, including secrets that may change Jake's -- and all those close to him -- thought that this may not just be a game.
The main protagonist of both the Game Freak and HACKED series, Jake is a hacker who accidentally created HAX and got sent into "The Game" to stop him. Though Jake acts like a hero, he just wants to help and often does the wrong thing.
The secondary protagonist of the HACKED series. A girl who once was a pirate who sailed Pixel Harbour, but now a thief who pickpockets to survive. She has a crush on Jake, who is oblivious to the fact.
The secondary protagonist of the Game Freak series, but one of the two tertiary characters of HACKED. Bob is one of the final two FuzzFlyers in existence and a cheery one. Similar to SpongeBob SquarePants, Bob rarely gets sad, as he is usually seen with a goofy grin on his face.
The tertiary protagonist of both the Game Freak and HACKED series, and Bob's brother. One of the two final FuzzFlyers in existence, Boeb has a dark and uncaring attitude. He is very calculated and unemotional, though deep down cares for his brother's safety. Sometime after Legend of the Sea, Boeb became a cyborg for an unknown reason.
A group of twelve artificial intelligence programs created to live like humans in their own virtual worlds. The Twelve are all numbered, and consist of both males and females. Among the Twelve, Jake and Autores are members of it.
The main antagonist of both the Game Freak and HACKED series, and Jake's greatest hacking achievement (albeit not on purpose). HAX rules over "The Game" with an iron fist, sending the world into a grey, dystopian society reminiscent of how futuristic Earths are portrayed in pop culture.
The secondary antagonist of HACKED, Dr. Tsupaiku is HAX's right-hand man, who invents crazy machines to help HAX continue on with his diabolical plans. He created HAX's bio suit, which allows him to have arms and legs.
One of HAX's greatest minions, and the commander of the Glitchers, Rocky is a tall, strong rock dragon. He fights using his rock-based powers, and uses two gloves invented by Dr. Tsupaiku to enhance his natural strength.
The first Glitcher ever created, Error is the insane brains of the secondary operation force, working with Rocky to command the majority of the Glitcher pawns. He fights using various glitches, and, like HAX, controls the environment around him.