The Heroic Brothers (Mario and Luigi)
The Mario & Luigi system has been re-used from Mario & Luigi: Superstar Saga, the commands are:
- Jump: The normal Mario and Luigi's attack.
- Hammer: The first special attack which the brothers gains, which Mario obtains on the Prologue episode, the Hammer system has been re-used from Paper Mario series, which the player needs tap A during a 15-seconds period.
- Bros Items: Returning from Mario & Luigi: Partners in Time, the Bro Items are back, with new ones.
Flower Power (Peach and Daisy)
Peach and Daisy's battle system are much more different from the Mario and Luigi system, the commands are:
- Star Power: Hold A to charge a power force, the Power Force is a projectile which is based on Peach's Beam of the Paper Mario 64.
- Perry/Darry: Works like Mario and Luigi's hammer, which Peach use Perry or Daisy use your Darry.
- Virtua Magic: This command can only be activated on the Virtual World, which works like the Bros Items.
Money Catchers (Wario and Waluigi)
Based on the they battle system on Mario & Luigi: Rivals Quest, they are the only ones which uses the X and Y buttons on the commands. The commands are:
- Dash Punch: Press X how many times you can in a 15-second time limit. When you finish Wario or Waluigi will do a Dash Punch.
- Shake It!: Based on the Wario Land: Shake It!'s Wario special move, Wario or Waluigi will get the enemy and to shake him press Y how many times you can in a 15-second time limit. This also makes the enemies drop coins.
- Catchy-a-tack: Works like the Bro. Moves in Mario & Luigi: Superstar Saga.
Truth Sidekicks (Birdo and Yoshi)
Birdo and Yoshi's battle system are completly different of the other's battle system. The commands are:
- Swallow/Egg-a-form: Birdo or Yoshi will sucks up the enemy in a similar way which Bowser swallows enemies on Mario & Luigi: Bowser's Inside Story, if you press B after you swallow a enemy, you can transform him into a egg.
- Egg Throw: If Birdo or Yoshi have any eggs, they can launch them into the enemies.
- Groundy Poundy: Birdo or Yoshi will jump on the enemy and do a groundy poundy, pressing B again, make them do a Groundy Poundy on the ground.