The following is a list of episodes.
Mario and Luigi are racing Wario and Waluigi when Bowser Koopa with Kamek attack. Meanwhile, Mecha Sonic nabs a Chaos Emerald from an unsuspecting Goomba.
The battle with Bowser begins, ending with Mario as the victor, thanks to a timely appearance by warriors from another dimension, Sonic the Hedgehog and Shadow the Hedgehog.
Sonic and Shadow recruit Mario, Luigi, and later Yoshi in the hunt for the missing Chaos Emeralds. Yoshi finds one, then is slaughtered into a coma by Mecha Sonic, spared only by the appearance of Mario, Luigi, Sonic, and Shadow.
As Yoshi recovers, the other four set out for more Chaos Emeralds with the help of Professor E. Gadd, who invents the Emerald Radar to help them find the Emeralds. However, the four Koopa Bros. from Paper Mario find a Chaos Emerald before them, and a fight ensues. Thanks to the Emerald's power, the Koopa Bros. win, and pick up the Emerald Radar as they hunt for more of these powerful objects.
Yoshi, fully healed, assists Mario, Luigi, Sonic, Shadow, and Professor E. Gadd as they journey to Yoshi's Island. E. Gadd has created the Radar Radar to find the original Radar, ultimately leading them to the Koopa Bros. There, they encounter the Yoshi Tribe, and after a short fight, the battle is stopped. The head of the tribe, Yoshi Chief, notices Mario as the baby he saved back in Yoshi's Island. Yoshi Chief explains the story of the Emerald, and five mysterious soldiers who took the Emerald and are enslaving the Yoshis to find more Emeralds. The heroes collect the Emerald resting atop a rock, but not before the Koopa Bros. appear and swipe it. Unfortunately, the Axem Rangers X appear, as the five enemies Yoshi Chief described. The Axem Rangers X get the newer Emerald and a battle starts.
A long and enduring fight ensues, as Wario and Waluigi wash up on Yoshi's Island. Without any luck, they notice the battle. After a long fight, which involved Mario and the Koopa Bros. dropping the Radar and the Radar Radar, Mecha Sonic interrupts, hitting the Koopa Bros. as they charge their super attack. Mecha Sonic also grabs the Axem Ranger X's emerald and uses them (along with the two in his possession) to transform into Semi-Super Mecha Sonic. In this form, Mecha Sonic is even more powerful than before, and easily kills all five Axem Rangers. Mecha Sonic then goes for the heroes, who survive the onslaught. With all hope seemingly lost, Mario and Luigi find a Power Star, which Mario and Sonic then use to temporarily go Super. It lasts long enough to nab all four Emeralds from Mecha Sonic, but not enough to destroy Mecha Sonic. Furious, Mecha Sonic kicks his almost-constructed death beam down towards the Island. Sonic tosses an Emerald to Shadow, who Chaos Controls everyone except the unconscious Koopa Bros. and the obliterated Axem Rangers X. In the end, everyone leaves safely with four Emeralds. The Yoshi Tribe departs from the heroes as Yoshi's Island is now completely destroyed. Wario and Waluigi escape the island, and managed to pick up the Radar Radar, now following the heroes.
The Emerald Radar Sonic picked up leads the heroes to their fifth Emerald, hidden in a Pipe Maze. They journey through this seemingly endless maze, and Wario and Waluigi try to follow but fail miserably. Luigi, Yoshi, and Shadow split up with Mario, Sonic, and the talking, traveling suitcase companion Stuffwell, who is carrying their four Emeralds. Mecha Sonic attacks, and to avoid the onslaught, Mario and Sonic go down into the nearby pipe... Stuffwell escapes with four Emeralds in tow. Mario and Sonic get trapped in this endless world known as World -1, World 36, or "The Minus World". This world is inescapable and 8-bit. Mario and Sonic meet up with two people also trapped, Goombella from Paper Mario: The Thousand-Year Door and explorer Kolorado from Paper Mario. After a long discussion, Sonic discovers that Kolorado is holding the fifth Chaos Emerald, who reluctantly hands it over. Mecha Sonic finds them talking, and a fight ensues, ending with Mecha Sonic as the victor. He uses the Emerald to Chaos Control out of there, but it doesn't work in this area. Enraged, Mecha Sonic promises to give Mario and Sonic slow and painful deaths. Meanwhile, Stuffwell finds Shadow, Luigi, and Yoshi, and head to the Pipe. Through communication they talk to Professor E. Gadd and Goomba professor Professor Frankly. They get a history lesson on the Minus World, but Shadow jumps in anyway, believing he can Chaos Control out of there. Yoshi soon follows, with Luigi refusing out of fear. Shadow and Yoshi join the fight but don't change much, and in a burst of courage, Luigi decides to jump into the Pipe. Luigi gets attacked by Bloopers when he enters. They cause him to jump out of the water. Watching the battle from the sidelines, Kolorado brings out his broken stopwatch. Luigi hits Kolorado by accident, and the stopwatch hits the ground, undoing the Negative Space temporarily. Everyone escapes, even Mecha Sonic, just in time. Shadow Chaos Controls everyone out of the Pipe Maze, and they arrive at Mario's house. As it seems things are getting peaceful, Peach's Castle is on fire. Toadsworth arrives and informs Mario that... the Princess has been kidnapped.
Bowser raid's Princess Peach's castle and kidnaps Princess Peach. Mario and the gang discover a letter from Bowser that he has kidnapped the princess. An argument with Shadow brews up, and Shadow leaves the team to find the Chaos Emeralds himself. With help from Professor E. Gadd and an invention, the heroes are able to reach the Omega Doomship. Surviving cannon and Bullet Bill fire by the ship, the heroes make it on and assault the army. They then reach a large room full of Koopatrols, and are able to conquer them thanks to the help of a Fire Flower that Sonic grabs. Just when victory is near, the leader, Basilisx, turns Luigi, Yoshi, and Sonic into stone and fights Mario. He is able to pin down Mario and is about to defeat him when the episode ends.