The gameplay is based off of the Mario & Luigi series. Similar to Partners in Time, there are two more characters (Sonic the Hedgehog and Miles "Tails" Prower) who are controlled with the X and Y buttons, respectively. Mario and Luigi continue the trend of using the A and B buttons.
In battle, the characters each have the choice of two normal attacks, two series of special moves, the ability to heal and the ability to flee. The Mario Bros. continue the trend of having the Jump, Hammer, and Bros. Attacks, along with new Hero Attacks/Sidekick Attacks (a new ability that uses Mario & Sonic or Luigi & Tails). The Sonic characters start out with a spin dash, where repeatedly pressing the character's button strengthens the attack. Later on, the characters can use the homing attack, which is weak, but can be used up to 5 times in one turn (adding more damage as time goes along). They can also use the previously mentioned Hero Attacks/Sidekick Attacks and new Mobian attacks.
Outside of Battle
All characters start off with the ability to jump. The player can make the four characters jump at once by pressing the R button. Later on, more moves are useable. Mario & Luigi get hammers and the Ball Jump. Sonic & Tails will unlock the ability to use non-battling enemies to cross spaces using a homing attack. The third set of abilities for them is the Spin Dash (which can take the four in a straight line similar to the Pegasus Boots in The Legend of Zelda) while Tails can make the four glide over certain areas similar to the tornado move in the Mario & Luigi series.
Tornado Levels are new to the game. The are side-scrolling areas that require the 3ds to be turned 90 degrees and to use the touch screen. The characters control a plane and can both dash and shoot through flying enemies, until a boss appears requiring to be defeated. This happens five times in the game, but can be replayed using the Showdown ring.
The story starts off on South Island. It shows Sonic and Tails running through Green Hill until they see a herd of animals running away from the woods. There shows Dr. Eggman in the eggmobile kidnapping animals to turn them into Robots. Sonic then proceeds to battle Eggman in a tutorial battle. Upon being defeated, the eggmobile explodes and is seen flying away to the sky. Tails wonders where he went. It then shows the eggmobile heading towards Bowser's Castle. It shows Bowser still mad Mario beat him after his last adventure. When his minions try to cheer him up, he says they don't understand having to battle a guy every time and always lose. As if on cue, Dr. Eggman crashes through the wall. Not knowing each other, Bowser yells as the doctor for breaking a wall in his castle. It shows bickering as the screen fades to black.
Meanwhile, Mario & Luigi are arriving at Peach's Castle, ready for a nice meal with the princess. As the two explore the castle, they find Starlow. The three enter the main dining room to find the Egg Carrier outside. It then shows Dr. Eggman claiming he can show Bowser who the real villain is. A series of robots flow out. After fighting their way through the castle, they find the Egg Prison, a weaponized suit that doubles as a prison. After destroying the machine. Mario jumps outside and uses a Super Leaf and a Super Star. Mario then rushes through the ship several times until it starts breaking down. Dr. Eggman barely escapes using his Eggmobile. Peach thanks Mario with a kiss.
Sonic and Tails are still in Green Hill Zone relaxing. It is then that they see strange creatures looking like turtles and mushrooms trying to kidnap animals. The two go through Green Hill fighting against any enemies in their way. Along the way they find a bunch of strange attack pieces. Upon finishing them, they build a Fire Shield. Sonic and Tails close in on this new villain known as Bowser. Bowser comments, "Kidnapping Animals? How does that loser think this is evil?" He then notices the two strange animals and sends in Petey Piranha to destroy them. The two are succeful at defeating it. They then break apart the cage holding the animals. Bowser jumps in to his Koopa Clown Car to escape.
At Bowser's Castle, the two villains understand one another finally. Then Eggman gets the brilliant plan. Have the heroes fight each other and finish off the weakened winner. At Peach's Castle, Mario & Luigi are seen having a nice dinner with the Princess. Then, Sonic comes in and kidnaps Peach. Meanwhile, Amy has finally caught up with Sonic. She starts hugging him much to Sonic's irritation and Tails' humor, when Mario comes in and kidnaps Amy. Mario jumps into a Junior Clown Car to the Mushroom Kingdom, causing the hedgehog and fox to chase after them in the Tornado. They land the the Mushroom Kingdom, looking around for the person who kidnapped Amy. Meanwhile at Bowser's Castle, Mario and Sonic come in holding Amy and Peach, respectively. Sonic presses a button on his wrist, revealing himself as Metal Sonic. Mario twirls around, splattering paint everywhere and turning into a watery blue Bowser Jr. With the trap in motion, the four go to Toad Town to witness the battle.
The two duos meet up at Toad Town. A battle then ensues (with the player deciding which team to play as) and finishes with the loser colliding into a toad house. They start to fall onto a toad family. Mario tries to hold up support as long as he can while Sonic ran inside getting the toads out. Realizing that they were both superstars, they try to find out who kidnapped Peach and Amy. Meanwhile, Bowser is mad until Eggman reveals something he was planning to do in the mushroom kingdom anyway. Ressurect the Dark Star.