For a 2D game I'd say something like this might work:
Mario and Luigi are relaxing at their home when suddenly a group of 7 Toads dressed in odd dark suits comes screaming at their house, warning them that Bowser is attacking the castle; the bros rush towards it (with various stages to play like your typical World 1, except with no fortress but instead Kamek would use her magic on a Piranha Plant to allow it to be giant and use its roots to walk, as a new boss).
Once they reach Bowser and they defeat him, however Bowser manages to sprint towards Peach and grab her at Mario's surprise, however it turn out that the group of Toads that warned Mario about Bowser knew that Bowser would have confronted him at the castle and they managed to sneak inside's Bowser's ship using some jetpacks they built while he was distracted fighting Mario. They throw a huge cage towards Mario, Luigi, Peach and Bowser (with Bowser still holding Peach with him) but Mario and Luigi manage to avoid it, resulting in Peach and Bowser getting captured and lifted up Bowser's own ship.
After that they told them their evil plan: they are a bunch of magicians and intellectuals who betrayed Peach, they say their studies have led them to believe that some ancient legends regarding huge beasts living outside of the Mushroom Kingdom might actually be true, with that in mind they plan to use their magic to hypnotise such beasts to get control over them and use them to bring the Mushroom Kingdom to its knees, such creatures were referred to as the 7 Great Beasts.
After they flee, Mario and Luigi are given a boat by a group of Toads that can allow them to follow the group of evil Toads outside of the Mushroom Kingdom to a group of islands nobody has seen before.
Here they travel trough the island (with 7 Islands, each one acting as a world) and it turns out those are the islands portrayed in the ancient books, the islands are:
1) Sandol (typical sand-themed World 2, only with a more old-wild west feel to it rather than egyptian, as it resembles more the old wild west than a desert, the Beast you fight in this island is Sandug, the giant sandworm-wiggler which attacks you by jumping out of the ground)
2) Leafon (a forest-themed stage set on top of huge trees, the Beast of this area is Colmeleon, a giant rainbow chameleon)
3) Fritz (an ice-themed stage set in a tundra/forest, the Beast of this area is Fayricle, a large dragon which a deadly ice breath)
4) Bitsies (small little rocky islands that serve as the water world, the Beast of this area is Bloogod, an enormous black Blooper with incredibly long tentacles)
5) Toty (a mountainous area with many rocky sections and remains of an ancient civilisation that has build cities in stone that serve as maze-like stages, the Beast of this area is Flonto, a large white eagle capable of casting huge winds)
6) Meccht (an industrial/mechanized area set on a huge complex of abandoned machinery, the Beast of this area is Tok, a huge robot spider)
7) Folhit (a fire/volcanic themed area with many rests of ancient cities destroyed by eruptions, the Beast of this final area is Good, an incredibly large fire-breathing dragon)
After Mario defeats the Beasts and sets an end to the group of Toads' evil plan, he is asked by a Toad wearing a cloth to follow him; he follows him trough a cave where he enters a portal of light and finds himself in a roman-styled city set above the clouds called Flontia (which basically acts as World 9), here he is cheered for defeating all of the Beasts and he is challenged to become a true Hero by completing the excruciating obstacle courses the ancients built. The Boss of this area is a large mech built by the Toad sages as a final test to prove the Legendary Hero's strength)
