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Story
Mario (or Luigi depending on who the player is playing as) and Princess Peach are walking together around Peach's Castle, when a mysterious thundercloud appeared, and struck the castle with lightning. Mario/Luigi went to investigate, and while he is there, Bowser Jr. sneaks behind a bush and kidnaps Peach. Mario/Luigi follows, and Bowser Jr. drags her behind him through eight different worlds.
The end of the first world has Bowser as its boss, unusually. Even more surprising, after Mario presses a switch that destroys the floor and Bowser falls into the pit of lava, the king's flesh is burned off and he becomes a Dry Bones-like version of himself (known as Dry Bowser). Later, at World 8, Mario has to face this undead version of Bowser as the penultimate boss in the game. Dry Bowser falls into a pit, but Bowser Jr. somehow finds his father's bones, and he revives him by tossing his remains into a bubbling cauldron, which results in not only Bowser returning from the dead, but growing roughly three times his size.
At the end, Bowser and his son fight Mario together, but Mario defeats them, sending the two into yet another pit. After the ending sequence, Bowser Jr. is shown dragging his unconscious father across the castle floor. When he notices the player watching him, he shouts something and then continues on with his task.
Items
| Item | Function | Sprite |
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| Super Mushroom | Turns Mario or Luigi into Super Mario or Super Luigi. | 
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| 1-Up Mushroom | Gives Mario or Luigi an extra life. | 
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| ? Block | Gives Mario or Luigi a coin or an item. | 
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| Big Star | A set number of these must be collected to win (only in Mario vs. Luigi mode). | 
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| Blue Shell | Turns Mario or Luigi into Shell Mario or Shell Luigi. | 
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| Brick Block | Breaks or gives Mario an item. | 
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| Coin | Collecting every 100 of these give Mario or Luigi an extra life. In Mario vs. Luigi mode, collecting 8 coins gives Mario or Luigi an item. | 
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| Fire Flower | Turns Mario or Luigi into Fire Mario or Fire Luigi. | 
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| Mega Mushroom | Turns Mario or Luigi into Mega Mario or Mega Luigi. | 
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| Mini Mushroom | Turns Mario or Luigi into Mini Mario or Mini Luigi. | 
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| Red Ring | Makes 8 Red Coins appear. | 
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| Red Coin | Collecting all 8 Red Coins that appear after passing through a Red Ring gives Mario a Super Mushroom, Fire Flower or 1-Up Mushroom, depending on what power-up Mario or Luigi is currently using. | 
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| Silver Coin | Just like normal Coins, but appear by hitting a P-Switch. | 
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| Star | Turns Mario or Luigi into Invincible Mario or Invincible Luigi. | 
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| Star Coin | Three of these are located in every course in hard-to-reach or hidden areas. They are used to remove Star Coin Signs and purchase different touch screen background skins. |  |
Glitches
Above the Ceiling
In World 3-Tower the player must go along the way until they fight Bowser Jr.. Step on him twice. Then he will go his usual routine trying to jump on the player. Time it right so when he jumps to the highest point, the player can jump on him. Also the player must use the technique where they can jump higher off an enemy. Aim towards the ceiling, if done correctly, Mario should be on top of the roof. The usual animation of Bowser Jr. running away will show and the Mario face signal turns halfway because the player can't see Mario.
Bowser Jr. Knockout
In any of the first Bowser Jr. battles (ones where he doesn't throw green Koopa Shells.), if the player has a Mega Mushroom in stock, the glitch becomes possible. When the player is in the battle and activates it, eats it, and stands still, when Bowser Jr. touches Mario/Luigi, Bowser Jr. will become unconscious. If the player waits until they turn back to normal, and jump on Bowser Jr., this will make him knocked out on the floor. Even if the player is jumping on him won't do anything. The only way to attack him then is to do a ground pound.
Door Glitch
If Mario or Luigi touch in an enemy, and in the same time enter in a door, when come in another side, he loses his power up, or become a Small Mario/Luigi, if don't have a power up.
Fake Spikes
In some levels, when Mario is Shell Mario, after ground pounding on spikes, Mario doesn't get hurt. However in other forms he does take damage.
Frozen Ghost House
Playing as either Mario or Luigi in World 4-Ghost House, the player has jump onto one of the spin dials that turns around and takes the player to the next room. However the player must jump right on the very left or very right of it, then jump straight off. The whole room will freeze. The player can smash blocks but they will be frozen as half destroyed blocks. The player can also fire fireballs but they will freeze too. If the player goes on the spin dial properly or touches an enemy the level will go back to normal.
Music Keeps Playing After the Final Boss is Defeated
If the player uses a Mega Mushroom to beat Bowser, then defeats Bowser Jr., the final boss music will continue playing.
Neverending Level
While doing the Walking on Midair glitch, if the player is Super and runs into a certain Piranha Plant at the right time they will end up on top off the level and can't go off the cliff face.
Saving Peach without Actually Saving Her
In the final fight, if the player defeats Bowser and then uses a Mega Mushroom, he/she has to jump on Bowser Jr. and hold the jump button. The player should make sure he/she's right next to Peach's platform and jump to the right as far as the player can. If the player did this correctly the player should be on the same platform Peach is on.
"Stuck" Between Blocks
This glitch can only be performed in World 1-4. The player must have a Mini Mushroom in their backup, then must play the level normally up to point where the Koopa Troopa is needed to break the formation of blocks. They must wait until the Koopa Troopa kills itself and drops down to the lower two blocks left. On the right block, they must Ground Pound and Jump, and should hit a hidden block (the player might go through the wall if you time it right). Then, they must use the Mini Mushroom and jump above the left block. The player'll be "stuck" inside the two blocks.
Through the Ground
In W1-Tower, if there is a flying ? Block,
the player have to hit the block so that its top is 1 pixel above the
blue platform. Then he or she jumps on the empty block and walk towards
the center of the platform and possible go through the platform. If not,
the player can try again by jump at the block and walk to the middle
again.
Trapped
This glitch happens in World 4-Ghost House, and Mario or Luigi need a Mega Mushroom in the character's item slot. They should go to the place where the "Frozen Ghost House" glitch happens (the "room" with the single Boo and invisible blocks in it), and go into the next room (the one that is barren except for a Balloon Boo and a one-way platform). To start the glitch, they should apply the Mega Mushroom and go onto one of the objects that takes the player go to the next room "properly". They will have their head stuck in a pipe. They can't move horizontally, but they should attempt to jump to start the glitch. Mario/Luigi will not be able to jump, and they will be taken back to the previous room. To fully activate the glitch, they should jump off and the spin dial will go the previous room. All they can do now is exit the level, or if they haven't completed the level, the player should wait for time to expire.
Under the Flagpole
In World 2-5, use the cheat to make the camera only move right (L R L R X X Y Y on the map after completing the game). The player should have any power-up (Excluding the Mini Mushroom). The player should go through the level until the player sees a Boomerang Bro. The player should go to the right of where it was, and jump into the quicksand. The player must keep hold of right on the D-pad while the player is sinking. When the player starts to move, Mario or Luigi should still be keeping hold of right, then the player must press A. Mario or Luigi will appear in a place that has gray blocks behind them, as they have to go down. The player should go on a Blockhopper. The player must jump when they are near the ceiling near a Star Coin. The player must keep jumping until they're stuck in a rock. The player will be at the end of the level, and under the flagpole. The player should jump when the player is not moving and then the player will be past the flagpole.
Walking Backwards
In the World 4 map after unlocking a green Toad House, the player can put Mario/Luigi in the overworld map on 4-1 and press down on the D-pad. The player will now walk backwards until the player reaches the end.
Walking in Midair
In World 4-6 the player should go up to where there are three green pipes on a rock above, each with a Piranha Plant. The player should stay there and wait for Dorrie to leave. The player should wait about 10 to 20 more seconds. Mario or Luigi should go to the far left, but not on the ledge. The player should run and jump, if the player is far enough Mario/Luigi should be walking in the air. However when the player gets to the pipe Mario or Luigi will be teleported to somewhere and the player will be invisible and unable to move.
