Mushroom Kingdom
The game starts with a short clip that introduces princess Peach's latest dilemma -- to which, you (mario) are summoned and are tasked to resolve while playing the game. It all starts as the goodwill ambassador from the Beanbean kingdom pays the princess a visit. Although this gesture was supposed to improve their ties with the mushroom kingdom, in reality, it was a cover-up to have them granted an audience with princess peach.
As it unfolds, the visitors lure princess peach from a supposed gift from their queen. As they open the treasure chest though, a jack in the box pops out from it, spraying a poison cloud in princess peach's face. A second scene is then pitched showing toad (mushroom) in panic, frantically looking for mario for help. This pitches in a short player-control where you get to use the directional jog to move around toad inside Mario's house. Go towards the left most part of the house where the bathroom sits. As you reach the bathroom, you'll hear someone humming. Once you check what's inside the shower, you'll be forcing Mario to end his bath and check out on you. With this, the message would've seemed to be relayed to Mario as he rushes towards the castle.
The third scene is held inside the castle once more. Now, with Bowser inside, which looks like another issue that needs to be settled. A short battle scene will take place - probably showing you around it's battle sequence format. Basically, you'll be taken for a spin of its mechanics and control during this period. Similar to mario's signature way to defeat his enemies, you'll engage the enemies in a turn-based battle using a stomp attack (or a combination of it). After the battle is settled, you'll be briefed with the the actual situation. This time, Bowser has actually nothing to do with it. Since Bowser couldn't perform his usual plans (of kidnapping) to princess peach this time, he'd decided to lend you help instead.
It turns out, some sort of spell has plagued princess peach - which took her voice. At the same time, whenever the princess tries to speak, bombs come out from her instead of her actual voice. Bowser decided that it isn't going to be of any use to him kidnapping peach in her current condition as it could spell disaster in his own kingdom -- so he lends you a helping hand. Off you go to the mission to take back the princess's voice and Bowser decided he could give you a lift on your way there with his Koopa Cruiser.
Mushroom Kingdom Plaza
As the situation has panned out, you are given time to check on stuff and roam a bit on the kingdom's plaza to warm up and figure out some of the basics. You are also hinted by toad to speak with everyone there. first off, you head on the left most part of the plaza, a mushroom there will ask you to show your jump to him -- which basically teaches you how to jump while you are roaming. This will give you the ability to jump on ledges and climb stuff like the bushes on the walls of the plaza. Head north and find the green mushroom there that is trying to look for "something precious". Take note that oftentimes, there are options for your response to ticket questions of some of the NPC characters in the game. For this instance, you may choose to help him, or to refuse to do so. If you help him look for it, head down the south-most part of the bush your currently in.
Performing on the simple tasks in this plaza basically teaches you the basics of the game, and at the same time rewards you with stuff. Whenever you approach suspicious looking areas, the Action Icon changes. Like in this pertaining task, when you reach the end of the bush, it will enable an action for checking it. When you find the item "something precious", head back towards the green mushroom and give it to him and he'll reward you with a 1-up mushroom. You may also check want to pop-up the "?" box near this area (you'll have to climb the bush and jump below it just like any other mario game), You'll have to jump from the bush you are currently stepping in to get there (run towards that direction and jump) since you won't be able to jump as high when you're from the ground.
Next, speak to luigi to point you where Bowser have gone, and he'll point you the direction. You use this on the following NPC you be talking to. Head right of Luigi and find one of Bowser's minions. He'll be looking for his boss and will ask you if ever you know where direction they went. Just tell him what Luigi told you, and you'll be rewarded by him later on in the game.
There is another pop-up box at the rightmost bush which will have a mushroom. Next, talk to the red colored mushroom near you and help him get the mushroom on the bush nearby. Instead of keeping it to yourself, try to give it back to him and he'll insist to have you keep it instead. Additionally, he'll reward you with a super mushroom as a send-off gift. That is pretty much in this area so head on north.
On the next area, there will be a save point from which you could save your progress. Just approach the floating book labeled "S" to save your game. As you head out north, a mushroom will catch up on you and give you a suitcase - which will contain everything you'll earn in the game. To access your suitcase, you'll just have to press the start button at any point in the game and check the menu screen. From here, you'll get to access the Items you've picked up in the game, and even change your clothes. You may also use this screen to check up on your characters' status. Additionally, this mushroom guy will give you 100 coins as a send-off gift.
Head on north and pick-up on the following scene where you'll be boarding Bowser's ship, the Koopa Cruiser.
Koopa Cruiser
Continuing where you left off, you find yourself inside the Koopa Cruiser. There will be a P.A. system addressing you to check your stuff before we reach the Beanbean kingdom. Also, you might want to save progress too on the save point above. When your done, head on the exit on the right. As you get out of the room, there will lots of Bowser's minions in here to speak to. Basically, these minions give you a hint to some of useful controls in the game such as jumping simultaneously when you are controlling both luigi and mario by pressing the "X" button, what controls the lead guy (in this case Mario) and the guy at the back's (Luigi) actions (A and B buttons).
Head out northeast to spot two more minions discussing about the "Bros. Block". Initially, the block will show which direction it'll go first. In this case, the blocks will move on the right. When it changes color, situate the character with the same color below the pop-up box and jump at it. When the right colored guy hits it, it may or not change color, and depending on how the box responds to the action, different button response will come from the player. In the given instance, every time you hit the box, it'll change color which then pass it back and forth mario and luigi -- suggesting the alternate press of the buttons A and B. Make sure you set them in the proper orientation for this too.
Head south and make your way to the exit on the right. On the following room, you'll see Bowser's minions taking pictures for their passports for the Beanbean kingdom. When you try to get past them, you'll be called out and asked whether you have your passports with you. Basically, you'll be introduced with these passports which show you your characters' stats in the game. All you need now is a brand new picture for the passports -- which is what these goons are there for anyway. You should line them up for their photos to be taken individually by standing on the marker on the ground for a few seconds - avoiding any sort of movement.
Head north and hit the pop-up box for a mushroom, and then head on to the southeast side of the room. Here you'll see another minion and try to speak to him. When he notices you, he'll introduce himself as the guy you helped back in the mushroom kingdom's plaza. For helping him, he'll reward you with a 1-up mushroom. Hit the pop-up box near him to earn another mushroom. Next, head out north and find your way to the stair out there. When you get in this next room, you'll have a few encounters teaching you the basic make-up of battles in the game. When you approach a barrel, an action button which will lead to to destroying it and be called out by Bowser's minion in the area. He'll introduce you with the battle mechanics when playing two characters in the game. Upon subscribing to this info, you might want to break the barrel near you to practice this as a battle will initiate after finding some Goomba minions inside the barrel. Barrels/Items that can be broken are colored differently to easily spot them. Additionally, you may jump over enemies to engage them into battle.
Every update on your game encounters will also record a knowledge-based battle-guide which will then be accessible via the "Guide" at the bottom screen (of the NDS). This battle will also be your first ever full-fledged battle in the game, as you'd actually earn experience points upon finishing the battle this time. Now head south an break another barrel there for another encounter (with Goomba minions). Remember, every encounter will reward you with experience points which will eventually earn your character a level up (so you might want to keep fighting in the game). Leveling up will give you a pre-determined upgrade on your stats plus the chance to additionally upgrade any one of the character's stat points via spin (values 1 to 4).
Move towards west, and find some of Bowser's minion to help there. Basically, he will teach you how to engage battle on enemies roaming the platform - which is simply by stomping them. Also, if you jump on a foe to start a battle, you can get an early strike on them. Finish off by tackling the other Goomba minion there and finishing the battle. After this, head further south and climb the stairs there. Upon reaching the next room, there will be a minion giving you some pointers on how to save progress within the Beanbean kingdom. Additionally, there is a save point above. Head west and talk to the minion situated near the hit box. He'll introduce you with this type of hit box where it triggers an action within the game. In this instance, it'll activate the grabbing crane mechanism of the ship and grab luigi by mistake. This will then lead you to the next scene on the deck of the ship.
Here, you'll be greeted by the Beanbean perpetrators and will be engaged by someone called the Great Cackletta. He'll basically brag about his greater plans of using Princess Peach's voice for his desires and end up calling out on his subordinate called 'Fawful"to attend to you. He instantly incapacitates Bowser which leaves the two of you to engage him.
The battle will have 2 parts. In the first part, he'll be equipped with a jetpack like weapon which shoots out a green colored cloud. By hitting him 3 sets of attacks in a row, you'll be able to destroy his equipment - which will lead you on the second part of the battle. During the first battle sequence, Bowser will offer a cover up when Fawful attacks you. You may simply chose to decline this offer. On the second part of the battle, the enemy attacks by egg rolling towards you. Three full sets of attacks (and counterattack) will defeat him - leading him to call-out for his headgear and escape the battle and target the Koopa Cruiser instead. The ship will ultimately fail and will explode mid-air, then leaving you crashing down the outskirts of the Beanbean kingdom, the Stardust Fields.