Mario and the gang are in the castle when a ship comes and the skies turn grey. The ship tells them to surrender, but they decide to not surrender. The captain tells them that unless they get all 7 Legendary Silver Stars that they will attack the castle. The mysterious captain yells that they have seven days to get the stars, one star per day. The gang starts the adventure, but Mario drops a fire flower, and a Goomba eats it, turning into a new fire Goomba. This reveals that enemies can now use power-ups.
Luigi decides to give Mario a day off, and a supply of power-ups are with him. On the day, Luigi runs into a switch, wondering what it does. The seven silver stars (which, in this game give power and power-ups to the Mushroom Kingdom and don't allow enemies getting power-ups if they are all together) are released, and Luigi runs to Mario, who notices the stars. He decides to go look for them. The same ship from the WiiU version comes, and gives him a map to find all the stars.
- Toad Brigade
Worlds are actually replaced with days in this version.
Hub World- Princess Peach's Castle- Intruders are entering the castle!
Day 1- Stormy Mushroom Kingdom- The first Silver Star is hidden in the Mushroom Kingdom, but it's stormy today.
Day 2- Chocolate Glaciers- Try not to eat to much of it! Get it before the chocolate melts!
Day 3- Yoshi Egg Galaxy- From Super Mario Galaxy, after one star is destroyed, maybe they can find a new one being hatched!
Day 4- Beanstalk Skies- One Silver Star sure is a high-flier!
Day 5- Time Workshop- You find the star at the start, but you're trapped! Can you get out with time?
Day 6- Vortex of Swirls- You found your way out of time, but now you're stuck in a vortex to get to Day 7! The sixth star just happens to be here...
Day 7- Piranha's Mouth- The last star was eaten by a Piranha Plant! Can you find it in the stomach?
Day 8- The Mysterious Ship- The captain wants the stars- but the Mysterious Captain is evil!
Hub World- Silver Star Cage- You can see your progress and do more boss fights in this world!
World 1- Uncontrollable Mushroom Kingdom- The weather and everyone has gone crazy!
World 2- Ice Cream Mountain- The frostiness, the creaminess... Just imagine. The delicious flavor. But don't eat it- one might be the star!
World 3- Rosalina's Comet- Uh-oh, the galaxies have TONS of stars! But one just might be here!
World 4- Old Clockworks- This time is messed up very badly!
World 5- Swirly Vortexia- A world full of strange vortexes.
World 6- Piranha's Stomach- This piranha plant sure has a big stomach!
World 7- Mushroom Mine- The last star was buried in all these rocks!
World 8- Oceans Ahoy!- The Captain stole all the silver stars for himself! Find his ship!
- Super Mushroom
- Fire Flower
- Ice Flower
- Super Acorn
- Mega Mushroom
- Mini Mushroom
- Baby Silver Star (Invincibility Star)
- Silver Star Switch (No enemies can use power-ups for 30 secs, but if an enemy gets it, you can't use power-ups)
- Goomba Hat (Makes you look like a Goomba, enemies won't attack unless powered up)
- Goomboth Hat (Makes you look like a Goomboth, no enemies attack)
- Combine Mushroom (Can combine two different power-ups that aren't stars or is the Super Mushroom)
- Flame-Freeze Mario (Combine Mushroom. Throws a fireball and snowball at same time)
- Fire Flighter Mario (Combine Mushroom. Flies and throws fireballs)
- Volcanic Mario (Combine Mushroom. Is giant and throws giant fireballs)
- Torch Mario (Combine Mushroom. Is small and throws tiny fireballs)
- Powered-Up Goomba Hat (Combine Mushroom. Makes you look like any powered-up Goomba and no enemies attack except powered-up ones. Also has qualities of power-up)
- Powered-Up Goomboth Hat (Same as Powered-Up Goomba Hat, but no enemies attack)
- Hibernation Mario (Combine Mushroom. Can fly and throw snowballs)
- Glacier Mario (Combine Mushroom. Giant and huge snowballs can be thrown)
- Ice Berg Mario (Combine Mushroom. Small and throws tiny snowballs)
- Pilot Mario (Combine Mushroom. Giant and flies.)
- Wind Mario (Combine Mushroom. Small and flies.)
- Opposite Mario (Combine Mushroom. Switches between big and little.)
- World 1: Wii U: King Lakitu. 3DS: Puff n' Huff.
- World 2: Wii U: Chocolate Miner. 3DS: Giant Scooper.
- World 3: Wii U: Dino Piranha. 3DS: Cosmic Mario.
- World 4: Wii U: Prince Lakitu. 3DS: 13 o' Clock.
- World 5: Wii U: Classic Bowser. 3DS: Worm and Mole (Wiggler and Monty Mole)
- World 6: Wii U: Black Hole. 3DS: Old Toad.
- World 7: Wii U: Giant Can. 3DS: Minor Miner.
- World 8: Wii U: Various Shroom Pirates. 3DS: Bowser Jr.
- World 1: Wii U: Lakithunder. 3DS: King Lakitu.
- World 2: Wii U: Suite Tooth. 3DS: Cheery Cherry.
- World 3: Wii U: Firey Dino Piranha. 3DS: Cosmic Bowser.
- World 4: Wii U: Lakithunder (again). 3DS: Father Time.
- World 5: Wii U: Powered-Up Classic Bowser. 3DS: Worm-Mole (Worm & Mole mixed together)
- World 6: Wii U: King Voltz. 3DS: Tongue/Petey Piranha
- World 7: Wii U: Giant Tooth/Petey Piranha. 3DS: Major Miner.
- World 8: Wii U: Shroom Captain X/X-Shroom. 3DS: Silver Star Bowser/Silver Dry Bowser.
- Squawk the Hawk
- Mouse Kateer
- Inky the Blooper
- Wario and Waluigi
- 2 False Bowsers
- Fake Silver Stars
- Toadlord, the Silver Star Keeper (must finish game and be Luigi to play)
- Koopa Troopa
- Many other enemies from past games, including Piranha Plants, Goomboths, and Paratroopas.
- The 3DS version is said to be a continuation of the WiiU version, because at the end of the WiiU version, a shadow figure jumps into the ship, said to be Bowser, and The Toad Brigade helps Mario put the silver stars into storage, and the land returns to normal. In the Petey Piranha boss fight in the 3DS version, Petey also says, "You won't defeat me like you did when I ate that bad silver thing!" The 'bad silver thing' could have been the star. X-Shroom is a boss in both.
- Various websites say that the game has totally different stories, but so much similar worlds/days.
- Owners of the WiiU version (and not the 3DS) may see a Silver Star Switch, which may confuse the player because it isn't said in the WiiU version that the Silver Stars stop enemies from getting powers.
- A hub world was added in the last version of the game, and there are a few bonus boss fights and adventures you can play there.
- A 9th world, known as Silver Star Cage, was originally going to be in the game, but it was mostly boss fights and changed it to a hub world.