There is an entire essay’s worth of fan fiction used as the description for this so bear with me here.
 
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After recovering from their unpleasant encounter with Bowser and his newly discovered powers, Mario and his new friends decided that they needed to combine forces in order to stop the latest threat to Equestria. The enemy’s troops were already infiltrating the peaceful lands of ponydom, and with Princess Luna weakened from the Koopa King’s stealing of her stars, Celestia’s grip over the kingdom would be fading fast. It’d only be a matter of time before Bowser’s army would soon be marching upon the steps of Canterlot.
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Twilight wasted no time and began formulating a plan. While the portal to her home had been destroyed, the possibility of an alternate route through one of the Mushroom Kingdom’s many warp pipes was the perfect place for her to start finding a way back. Fortunately for her, the Mario Brothers (masters of plumbing) had knowledge aplenty regarding these tools of transportation, and together the two groups worked throughout the night mapping the various warp zones across the Mushroom Kingdom. After hours of what felt like running in circles in the castle library, a potential warp zone was discovered on an ancient map recovered from Rogueport. Much to nobody/pony’s surprise, the way to get there would require travelling across many lands.  
Having trekked much of the Mushroom kingdom, Mario was eager to start the adventure right away. Though he hadn’t known this odd-looking group of equines for very long, he had a good feeling about his four-legged companions. Any enemy of Bowser’s was an ally, and Mario felt somewhat responsible for Equestria’s invasion, as he had always taken it upon himself to stop Bowser and his antics regardless of where his evil conquest was next taking place.  
Mario’s enthusiasm however was outmatched by the yawning of his brother and the ponies surrounding him. It was far too late in the night to start a long journey, especially without the proper supplies and rest, as both Applejack and Twilight noted. While Rainbow Dash was also eager to get back home to kick some shelled flank, she knew it was probably best to rest for the night in order to get a fresh start the next day; she also knew it was unwise to argue with a sleep-deprived Rarity. Thus the ponies went to their accommodations in Princess Peach’s castle while Mario and Luigi left for home.  
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Luigi’s day had been more exhausting than usual. It wasn’t often that creatures from another kingdom dropped in, though when they did it was often with bad news: the Bean Bean Kingdom, the Sprixies, the Lumas and Rosalina, they and many others had all arrived bringing some form of unpleasant information (usually about Bowser). While he was usually gung-ho about accompanying Mario on another adventure, Luigi would be lying to himself if he claimed he was happy about this latest development. The only minute thing he had planned for that prior day was interrupted by a multi-colored group of talking ponies (surprising) and a giant, black and green-eyed Bowser (not so surprising). Mario jumping into the ensuing fray made his afternoon far more interesting, but Luigi’s picnic lunch was ruined regardless. It didn’t help his mood knowing that his favorite hill was now a smoldering piece of burnt grass.
Regardless of the previous day’s events, Luigi was happy that he was still in one piece, and that he would be able to face the journey ahead on a full night’s rest. As he began settling himself into his bed however, Luigi’s mind began stirring. Questions about who these ponies were and how they got to the Mushroom Kingdom began circulating in his head. The most distressing of the queries was regarding Bowser and his menancing new powers: What happened to his eyes? How come Mario, even with the help of those ponies, couldn’t stop him? Why were his eyes like a snakes? How did Bowser get to Horselandia (or whatever it is) in the first place? Why did his pupils glow? What gave him the ability to steal those stars in the first place? THEM EYES!?!
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The morning rays were just begining to peek over the hills just as Luigi’s mind had calmed down. Light began striking upon his face, forcing him to open his exhausted eyes towards the morning sun. Knowing that he couldn’t fight the dawning of a new day, Luigi forced himself up and out of bed. Grogilly, he looked around at his well-maintained room, taking in the silence and tranquility that welcomed him every morning. Knowing that it would be a while before he would be back in his place of serenity, Luigi allowed himself to soak in the homliness of his room for a moment longer before heading to the kitchen to brew some Woohoo Blend.  
Luigi returned with his coffee in hand, only to find that his brother and all the ponies had all managed to occupy his room. He had not even been gone for two minutes, and the place was already a mess of various items and power ups that Mario and he had found in thier many adventures together.  
Speaking of his brother, Luigi quickly scanned the room and found Mario sitting at a desk among a pile of powerups. Next to him was the purple pony (Twilight, was it?) who was levitating (LEVITATING?) a Fire Flower and scribbling notes into an especially large book. Looking around further, Luigi saw that the pony in the cowboy hat (who had a knapsack full of various goods) was talking to the pony in makeup, who was also levitating (LEVITATING!) a couple of gold coins. The rainbow one was busy pacing around the room while Fluttershy appeared to be trying to calm her down. She had an egg on her back (a gift from Yoshi?), cradled carefully between her wings (she must be very caring and thoughtful person…I mean, pony). The pink one with the curly hair, however, was nowhere in sSsiiIgghHtT!  
Luigi and the others felt a powerful rumbling coming from under the floor. A second later and an explosion of bed stuffing revealed an excited (and dirty) Pinkie Pie with a Spin Drill atop her head. Her overwhelming excitement quickly turned into intense emberassment upon seeing the blank look upon Luigi’s face.  
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Mario winced as Pinkie drilled through Luigi’s bed. Noticing the stares that the other ponies gave her, Mario figured that this type of behavior was sometimes typical from Pinkie Pie. He had learned earlier from Twilight that while she causes some occassional destruction, Pinkie’s actions were usually done out of the best intentions, to make her friends smile and give them hope in light of any situation they face. Mario was willing to accept these facts, but the recent use of the drill on the other hand didn’t really fit the “fun and hope” criteria.
To his credit, Luigi was handling the situation better than Mario had expected. His younger brother was often quiet and reserved, not especially open to sharing his feelings with others, and really didn’t like his privacy invaded. Mario felt bad about taking over Luigi’s space without permission, but his own room had already been filled to the brim with documents and maps scattered about from earlier that morning. He would definitely talk to Luigi about the bed and the use of his room later, but he was currently helping Twilight catalog all the possible powerups and items that they could need on their journey. After many, many adventures Mario had collected quite a few of unique and helpful items, some that cold prove useful for the journey ahead. The trouble then, Mario thought to himself, is deciding what to take. And fixing the bed, of course.
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