The story starts off with the final round of the tournament: Mario vs Sonic. After fighting each other, Mario/Sonic releases his opponent. Mario/Sonic awaits his prize of a trophy/chili dog.
But then, Nick Fury himself fights Mario and Sonic! Unbeknownst to everyone, he is a Imperium! The Imperium have been re-planning their return for a long time.
Just as it seems all is lost, the Primids come in. They suck up the stadium, and the fighters all run away. However, Mirania trips, and the two help her get up and get out.
Meanwhile... Homer Simpson is enjoying a doughnut when all the sudden the Kermit Mafia attacks! After defeating the Kermit Mafia, Homer goes out of the coffee shop only to meet Mordecai and Rigby. They point to the subspace bomb being planted in the town, and Homer and his new found friends try to rip the ROBs off the machines. After seeing they can't, they run. The bomb sucks up the town, and they barely get out alive.
Finn is saving the Candy Kingdom from a deer attack when he sees a large and flying ship named the Solar Sailer. The Solar Sailer drops a subspace bomb and Primids. Princess Bubblegum is abducted into the ship, and Finn gets grabbed by Jake, who pulls him out of the bomb's range.
Mario, Sonic, and Mirania find themselves in a tropical jungle, and suddenly Syndrome's henchmen come in and attack. While the group is able defeat a few, one nearly kills them but is stopped by Mr. Incredible.
Meanwhile, Homer, Mordecai, and Rigby stop at arcade where they are approached by CLU's henchmen. Almost unable to take them, they are saved by Quorra who tells that basically everything is hitting the fan. The machine that takes the user into the grid is now letting in programs into the real world. In a attempt to get to the machine, Mordecai and the others are sent into a deep sleep and are sent into the Solar Sailer.
Samus Aran in the meantime is in a research lab for TWO, which to his discovery has been taken over by the Primids. After defeating some, she heads off to find R.O.B fighting the Primids as well. Then, the Lizard shows up, and attacks them. After defeating the Lizard they head towards the hallway.
The Irate Gamer decides that breakfast is ruined and decides to beat up random people. The Angry Video Game Nerd and The Nostalgia Critic are fighting, and then the Irate Gamer bursts in. They decide to beat him up, and continue the fight.
Finn and Jake find a Nether Portal just outside the Candy Kingdom and enter in it. After fighting off the Nether creatures, they end up in Pennsylvania, where the Ender Colossus is destroying some of it. After defeating the Nether Colossus, they decide to head North.
The Irate Gamer regains consciousness and decides to take out both of the video reviewers with a trophy gun. However, Jake and Finn bust in and decide to help with the fight against the Irate Gamer. The Irate Gamer places down the Aladdin game and gets the Game Genie to fight them. After the fight with the Game Genie, The Irate Gamer snags the AVGN and Finn. After getting away, Jake and the critic team up.
Meanwhile on the Solar Sailer, Homer and the rest wake up. After fighting some of the ROBs and Primids on the ship, they head down to the lower levels to the engine room and shut it down. The ship is headed towards a crash course to Nomanisan Island.
Mario and the others see the ship and Mario, Homer, Mordecai, Rigby, Sonic, Quorra, Mirania, and Mr. Incredible decide to go find Syndrome's hideout. After defeating some Primids and henchmen, they reach Syndrome's headquaters and face off a Omnidroid. After the Omnidroid is defeated, they face off Syndrome, who is defeated and turned into a trophy. However, they can't stay prideful for long, as the Irate Gamer collects the Syndrome trophy and faces the group using the Pixel Demon.
In the meantime, Invader Zim is planning a invasion on Earth, working with the Subspace army. He reports to Tabuu, and releases a bomb in Pennsylvania. Jake and The Critic see the bomb and haul outta there. They go near a green hill, where they meet Tails. Suddenly, a land shark attacks! They defeat the land shark, and decide to rest until Domo-Kun suddenly starts attacking. After defeating the Subspace Domo, Domo joins the group.
R.O.B and Samus discover that three of the Titans are being used as research. Suddenly, a Primid releases the Titans. After defeating all three Titans, Medusa comes to pick up their trophies and attacks R.O.B and Samus. Despite Medusa not winning the battle, she disappears into the shadows and leaves Samus and R.O.B to fight a bunch of Heartless Shadows.
The Irate Gamer is on the run after Mario and Homer and the rest defeat the Pixel Demon. He drops a subspace bomb, but before it can be activated Mario pushes the R.O.Bs away from the machine. Deciding that he's had enough, Irate Gamer turns Mario into a trophy. Mr. Incredible decides to beat Irate Gamer into a trophy of his own. They free AVGN, Mario, and Finn, but before freeing Syndrome, Medusa reappears and grabs it. She disappears and leaves some Heartlesses behind. Mario frees Irate Gamer.
Meanwhile at the Mystery Shack, Mabel and Dipper see that some Primids are gathered over by the shack. After defeating a few, Gideon reveals himself as one of the masterminds behind the invasion. He then attacks the two, and is defeated and turned into a trophy. Just when the bomb is about to go off, Mabel and Dipper take the Gideon trophy and get into the kart with Wendy. They get just outside the radius of the bomb and are in a deep forest. Zim reports to his superior, Tabuu, that Gideon was just taken down. Tabuu tells Zim not to fail him again, and Zim begins to question his own leadership in the plan.
Meanwhile, Mario and the group go into New York, where they see Bowser commanding a army of Primids and Goombas. After fighting off 100 of the army, Bowser reveals he has trophies of Princess Peach, Princess Rosalina, Mai, Bonne Jenet, and Zelda. Despite everyone telling Mario and Luigi it's a trap, they go up to Bowser and try to defeat him. After jumping away into his get-away, Bowser reveals that the Princess Peach and Princess Rosalina trophies are possessed by Shadow Bugs. After defeating both, Medusa appears and takes the trophies of Mai, Bonne Jenet, Zelda, Princess Peach and Princess Rosalina. Mario decides not to give up, on continues into New York.
In the forest, Link pulls out the Skyward Sword, and continues to walk into the forest, bumping into Olimar. All the sudden, Primids come in and attack, but then Mabel and Dipper swing into the action. After defeating the Primids, Link, Olimar, Mabel, Dipper, and Wendy head off into a nearby telaporter.
Meanwhile, in a suburban town, Edd discovers his house is filled with Heartlesses. After defeating the Heartlesses, he heads off towards downtown, where he meets the Critic, Tails, Domo-Kun, and Jake. Suddenly, Hugo comes up attacks them. After defeating Hugo, they find a telaporter.
Homer and Mario and the others find Ned Flanders, who is trying to preach the word of god to Greg. Greg gets mad and attempts to kill Flanders. After defeating Greg, Ned Flanders joins the team. They see a large number of people coming out from a telaporter and run towards them.
The Critic, The AVGN, Mario, Homer, Ned Flanders, Link, Domo-Kun, Olimar, Mabel, Dipper, Edd, Jake, Finn, The Irate Gamer, Quorra, Mordecai, Rigby, and Mr. Incredible all team up. They then notice that another Subspace bomb is being planted. Out of options, it looks like they are doomed. Suddenly, Luigi comes from out of nowhere and warps them to a T.W.O research lab.
Samus and R.O.B are then swarmed by a large group of people, accidently freeing Beetleworx Abomination. After fighting him off, they move forward into the teleporter room.
Meanwhile, in a Ruined Zoo, Ness and Kumatora are fighting off the Primids, which now have taken over half of the world. White Mage comes to their rescue, and helps fight them off. Another subspace bomb goes off, but a smaller one.
Ralph decides to help out this world to become a hero, so he game jumps into Sparta, where he meets Leonidas. After defeating the Persian Empire, the Persian King reveals himself as Nazo and takes the Ralph and Leonidas trophies and then tries to warp to the T.W.O research lab, however Lyn stops him. After freeing Leonidas and Ralph, they head off to the Ruined Zoo.
Nazo awakens and goes to the T.W.O research lab. After being defeated again, he grabs the chaos emeralds in the lab and turns himself into True Nazo. After defeating the group, he warps them all to Subspace. Zim releases another Subspace bomb in Sparta.
Back in the Ruined Zoo, things are looking bleak for Lyn, Ness, White Mage, Kumatora, Ralph, and Leonidas. Pit and Palutena come down and help out the fight.
Meanwhile, Lucy Heartfilla is fighting off some of the ROBs that want to use a subspace bomb. She accidently kicks open a Xenomorph egg and fights off the Xenomorph. After freeing him from trophy state, they fight off Metal Mario and Hot Dog. They get warped to the Ruined Zoo, where they fight off Bowser.
Bowser is defeated and Rosalina, Peach, Mai, Bonne Jenet and Zelda are freed.
Rouge the Bat finds the Princess Bubblegum trophy and frees it. Medusa then tries to capture the two, but her trophy gun is destroyed. Mad, she fights them. She looses, and is freed. Medusa, Rouge, and Princess Bubblegum go to the Nightosphere and find Marceline, who agrees to help them.
In the Ruined Zoo, the Primids retreat. The group heads towards the Floating Island, where Subspace bombs are being deployed. After exploding it and getting ships, they head off to Subspace and are turned into trophies by Nazo.
Medusa frees her trophy collection of Syndrome, Endflux, Reptflux, Zelfux, Tifa Lockhart, and Captain Video. They head to Subspace, only to be turned into trophies by Nazo.
Nazo, Zim, Tabuu, and Darkseid remain. Darkseid says they are very close to conquering the world. Zim realizes this is a shared thing and bashes Nazo on the head, making Nazo recollect his memory. Nazo tries to defeat Tabuu, but Tabuu fuses with Darkseid and goes up against the traitors. Just when he's about to release a Omega Beam, he gets kicked by Sackboy. Sackboy then frees everyone. Tabuuseid, who's had enough of this nonsense, sends everybody into a Great Maze, in hopes that they die before fighting him.
After the Great Maze is defeated, Tabuuseid faces off the heroes and is left defeated. The world reverts back to the way it was, and everybody decides to go to Chick-Fil-A.
Tabuu lays defeated, looking up at Missingo, who shrieks and infects his body with glitches. Glitch!Tabuu stands up and displays the same shriek.
Everybody is waiting in a very long line to get food. The register constantly keeps looking weirdly at some of them.