In my head I see Tatanga as the next villain, and he hypnotizes the resident kingdoms to do his bidding.
A post-Bowser Fortress Brooklyn newscast with a montage from various headlines and media would be a great way to start the sequel as a way to establish the Mario Brothers becoming this overnight sensation, along with being New York’s top plumbers.
Daisy is introduced as a new resident in Brooklyn working part-time for Mona Pizza’s and Luigi develops an infatuation for her, all the while she’s intruiged as to where the Brothers head after-hours considering their fame (and the nature of the Warp Pipe as she discovers it).
A hypnotized Donkey Kong kidnaps Pauline at an unvieling of new construction plans on top of the Bowser’s Fortress Grounds. The classic Donkey Kong arcade moment is recreated (and later becomes an explanation as to why “Jump Man” gets renamed to “Donkey Kong”), but when DK snaps out of it, it was revealed all the Kongs have been subjugated by Tatanga via hypnosis, and DK used the Warp Pipes to try to warn Peach before he himself got struck with hypnosis himself while trying to escape. The Bros. decide to head back with DK to the Mushroom Kingdom and ask the Princess for aide, with a curious Daisy following pursuit unbeknownst to them.
However somewhere along the way, both Mario, Peach, and DK get kidnapped. We are left with a panicking Luigi and a clueless yet determined Daisy. An earlier scene in the castle would see her witness a shrunk down serenading Bowser still wanting to do anything for Peach, and Daisy gets the idea to free Bowser as a way for them to be able to pursue Tatanga. All three decide to sneak back to Brooklyn to “fetch” Bowser’s Castle before going after the mind-controlling alien, who is now targeting the Kingdoms of Sarasaland next. (At this point Daisy understands how Warp Pipes work well enough that they fire a Bazai Bill into it to teleport the Fortress back to the Mushroom Kingdom.)
I think the trio of Daisy, Luigi, and Bowser can play off each other really well. Luigi has to muster courage, and oddly gets some advice from his former nemesis, while Bowser gets love advice from Daisy. Along the way they find and ally with Yoshi, who seem to not be affected by Tatanga’s hypnosis.
…Yeah, I’ve been mulling alot about a sequel haha. But I simply don’t want Bowser as the villain in the next one.
Also the end credits to the sequel should play the Super Mario Land song from the Super Mario Compact Disco album.