This is part 1 for a synopsis of the hypothetical finale to the Mario franchise. Lots of revelations and character deaths to come.
The game begins with a celebration at the Mushroom Kingdom. Bowser has been imprisoned at Embrodia Confinement, a far away prison after his green troopa minions double crossed him and turned him into the good guys. The green troopas ally with the mushroom kingdom and they have a celebration because of this. During the celebration, Princess Peach and Daisy award Mario and Luigi the Celery Award, which is the highest honor in all of the mushroom kingdom for protecting the kingdom.
As the celebration progresses, the castle is suddenly blown to pieces killing everyone inside. Fortunately Peach and Daisy were out of the castle at the time. Right after this, Bowser shows up in flying ships along with Kammy Koopa, Koopa Kid, Wario, Waluigi, many new villains, and Donkey Kong after Bowser sided with his kind promising to spare his kind after destroying the world.
The green troopas begin to slaughter other toad creatures and it's evident that the green troopas are still loyal to their former master. Mario and Luigi fight their way through enemies attempting to get to Peach and Daisy. Donkey Kong, killing many citizens along the way, kidnaps both of them, bringing them back to the ships. Before leaving, Bowser tosses a floating spherical light into the middle of the kingdom, which turns black and consumes all of the kingdom, making the whole community vanish.
The screen goes black at this point, and while black, the player can hear a faint voice, whispering different unknown sayings. If the player pays attention, they'll recognize that the voice is Princess Rosalina.
When the screen cuts out of black, the player can see Mario, Luigi, Toad, Yoshi, and Toadsworth sprawled on their backs in a house. Princess Rosalina, some of her star minions, and an unknown good looking man carrying a bow n' arrow are standing around them. Rosalina mutters the word wake and the five of them do. They ask what happened and Rosalina explains that Bowser destroyed the Mushroom Kingdom once and for all. After mourning, Rosalina explains how she tried to save them the whole community, but only managed to save five. She says that Bowser has found a power source called Marmian that has a fission reaction so powerful that it doesn't explode, but just consumes everything in it's path within a ten mile radius. Bowser gets this power supply from a place called Nightmare Valley, which is a refuge for all of the nightmares people have thought up over the years. Marmian is in short supply and is expensive, so Bowser only has a handful, and plans to bring down the world with it.