When Bowser learns about a crystal star hidden in Peach's castle that can give a HUGE amount of power, he sets out to steal it. Mario and Luigi, Princess Peach, all the Toads, and Princess Daisy try to defend it. When Bowser finally gets Daisy to betray her fellow heroes and help him, he gets his hands on the star. He terribly mistreats the citizens of the Mushroom Kingdom. Mario, Luigi, and Peach must stop Bowser and Daisy and restore peace to the Mushroom Kingdom.
Mario: Hero and main character. He is the main help in defending the Mushroom Kingdom.
Peach: The Ruler of Mushroom Kingdom. She (obviously) helps defend it from Bowser. She is normally kidnapped by him, but in this case, he is trying to kill her along with the other heroes.
Luigi: Mario's bro. and a main help in restoring peace to Mushroom Kingdom. He is also said to love Daisy.
Daisy: While Daisy appears in her normal attire, a diffirent feature is her long hair. She looks like Peach's costume in SSBB, but keeps her own facial features and bangs. Daisy is and has been for a long time a friend of Mario. However; when Bowser tempts her with the stars power ("Bowser's Fortress"), she slowly turns to Bowser's side - against Mario. She hates Mario mostly after he replaces the star with a fake one, which is poisonous to the touch. She grabs it and is poisoned ("Castle Siege"), but Kamek is able to take her to Bowser, who heals her. She accompanies Bowser in his terrible reign over Mushroom Kingdom. With the power of the star, she is able to create lightning from her palms
Bowser: Main villian and rival of Mario. Bowser and his army of koopas end up capturing the Mushroom Kingdom ("The Darkness Begins"). Accompanied by Daisy, he rules over the Kingdom.
Bowser Jr.: Of course, Bowser's heir helps him take over the Mushroom Kingdom. He is the commander of the Koopa Army.
Morton Koopa Jr.: Son of Bowser, he helps try to kill Mario. He almost succedes, but is stopped by someone the Mario Bros. least suspected.("The Western Canyons")
Toad: Most Toads are warriors that will just fight by your side. This one in particular has no armor and is playable. He doesn't have much of an impact in the story, though.
Yoshi: Mario's good friend. He accompanies Mario on his journey. He runs into Mario in the woods, ("Old Friends") where the two of them spyon Bowser's army 's camp and hear the plans to capture the Castle at dawn, which succedes unfortunately.