You may start playing as Billy, Mandy, Grim, or Irwin, and start the game in Asgard. Someone released dangerous Mojo balls from Grims trunk, and they set off to find out who. They beat up Irwin in Asgard, but find only a chicken feather, leading Mandy to believe it to be Jack O' Lantern. They defeat him and for unknown reasons, head to the Underworld. They take down Nergal and Nergal Jr. and find more chicken feathers, taking them to the mutant chicken farm from a previous episode, Which Came First? Grim believes that they will find who did it at Billy's house, leading to a climactic battle with the Brain-Eating Meteor. Afterwards, it is discovered that it was Billy leading a trail of chicken feathers from a curse Grim put on his trunk giving Billy a chicken tail. He was digging in grim's trunk to free Mo and Jo. It then goes to the credits where you can play as Mandy, beating up Billy.
- Billy: Unlocked at the start
- Mandy: Unlocked at the start
- Grim: Unlocked at the start
- Irwin: Unlocked at the start
- Eris: Finish story mode with either Billy, Mandy, Grim, or Irwin
- Nergal: Finish story mode with either Billy, Mandy, Grim, or Irwin
- Fred Fredburger: Finish story mode with either Billy, Mandy, Grim, or Irwin
- Hoss Delgado: Complete mission 9, Tier 1
- Dracula: Complete mission 5, Tier 2
- Jack O'Lantern: Complete mission 9, Tier 2
- Nergal Jr.: Complete mission 9, Tier 3
- General Skarr: Complete mission 6, Tier 4
- Boogey Man: Complete mission 9, Tier 4
- Lord Pain: Complete mission 9, Tier 5
- Chicken: Complete story mode with all characters and play for 10 hours
- Nergaling: Complete story mode with all characters
- Viking: Complete story mode with all characters and destroy MOST letters in the credits
- Clown: Battle 100 times in VS Mode
- Pumpkin: Complete story mode with every character and get 100,000 damage points in VS mode
- Some of this games defeat quotes and opening taunts are references to the show, except for characters that did not appear alongside each other (like, for instance, Nergal Jr. and Fred). For example, in the intro to Evil Con Carne, General Skarr's profile says that he enjoys kicking puppies as one of his hobbies, which he declares in the game as an opening taunt.
- Some quotes are references to other media, such as Mogar singing "Me, rock you like a hurricane!" (a reference to Scorpion's "Rock You Like a Hurricane") or Irwin crying "For the horde, yo!" (a reference to the MMORPG World of Warcraft).
- No character can go into Billy's Backyard outside of Story Mode.
- The song by Purple Filth heard in Battle of the Bands is present in the credits.
- In an early version of the console release, Billy's Backyard (the final Story Mode Stage) had two players fighting. This could mean that the Story Mode could have had a co-op option, or that the stage could have been playable in VS Mode.
- Also, in several trailers and the demo shown if you leave the game remaining for a few minutes, the character icons are shown to be a bit bigger (and slightly different in some cases), and Grim's clown costume actually resembles what it looks like in the show. The reason for these changes is unknown, particularly the latter.
- While most costumes are based on events from the show, some costumes made their debut in the game (like Eris's goth outfit or Lord Pain's cowboy costume).