Dr. Heinz Doofenshmirtz has created the "Evil-Gathering-inator", which summons villains from different worlds to take control of worlds together. Heroes such as Perry the Platypus (Agent P), Randy Cunningham, Dipper Pines and Mabel Pines, Wander and Sylvia join forces to stop the villains and save their worlds.
It later turns out that the villains grouped together to save their worlds from the evil dream demon Bill Cipher, who has threatened all of reality with his powers and is held prisoner by the villains; and the heroes' fight against the villains has only freed Cipher from his dimensional cell, as he now plans to take over their worlds. Realizing their horrible mistake, the heroes go on to defeat Cipher, who then disappears away in anger and defeat, allowing both the heroes and villains to return back to their worlds.
The beginning of the game has a short tutorial stage led by Major Monogram from Phineas and Ferb. Each stage consists of two normal levels and one boss level (aside from the final stage). Each stage is maintained by one villain. Each normal level has a number of "spawners" that bring minions in to attack the player. The goal is to destroy all the spawners, and then the tower that appears in the middle of the room after defeating the spawners. Spawners appear on a pattern, sinking back underground after 5 or 6 seconds of being above ground. Spawners cannot be hurt while below ground. Boss levels usually consist of one main boss. Bosses can also spawn minions. The first stage is Gravity Falls, then Wander Over Yonder, then Randy Cunningham, and finally Phineas and Ferb. The bosses are the Gremloblin, Lord Hater's ship, a McFist robot, and a Norm Bot Smash-intator.
After defeating the Norm Bot Smash-inator, you receive a message from Major Monogram saying that you have won and that the next door will return you to Monogram. Upon entering it, you meet Bill Cipher, who reveals the villains teamed up to stop him and locked him up in a dimensional cell. But since you defeated him, he is now free! You now must defeat Bill. Bill has significantly more health points than all of the previous bosses, and is also harder to hit because he is behind a row of barrels. When he is mad the barrels will go away but he will be harder to dodge. After you defeat him, a picture appears with all the game's protagonists attacking Bill with a line saying "All of the heroes (and villains) returned to their home worlds...but none of them ever forgot the eye of the evil triangle guy."
- Gideon Gleeful's Gremloblin
- Lord Hater's Ship
- Hannibal McFist's Psycho-Bot
- Dr. Heinz Doofenshmirtz's Norm Bot Inator
- Bill Cipher
- Gravity Falls, Oregon - The Mystery Shack
- Random planets
- Norrisville - Norrisville High and McFist Industries
- Danville - Flynn-Fletcher House and Doofenshmirtz Evil Incorporated