For example I wanna label myself as the "Pacifist Nova" as I don't want to be the direct cause for any lives lost but will still point out if the wish kills 7 billion people.
Bowser finds out about Equestria from a troop of Magikoopas led by Kamek and decides to go investigate the place, sending Jr and the Koopalings with him. (Mainly because I think a Side plot about Roy hating Equestria and eventually becoming a fan of it would be funny). Bowser realizes that Equestrian magic is powerful enough to take over the Mushroom Kingdom so he tries to kidnap Celestia and Luna to takeover Equestria so he could declare war on the Mushroom Kingdom. It goes about as well as you would expect, and after getting his shit wrecked he meets Tirek, and the two of them agree to work together in exchange for helping eachother with their goals.
Meanwhile, Celestia & Luna summon the Mane 6 (plus Spike) to talk about the new threat, and Pinkie Pie gives a lore dump about Bowser, somehow knowing everything about him despite the fact they never met, because honestly, not only is it in character, I can't think of any other possible reason for them to find out about the Mario Bros. So the princesses summon the Brothers as well as Starlow and Peach. From there the gameplay would be like the original plan for Paper Jam with 4 characters controlled at once, the Mario Bros, Twilight Sparkle, and an interchangeable 2nd member of the Mane 6. Interactions between the cast, particularly Starlow and Spike as the guide characters and Peach and the princesses would ensue, the group visiting environments from both worlds.
The Climax of the game would have Tirek betray Bowser, taking the magic of not only him, but his entire army, in addition to the magic of Celestia, Luna, & plenty of background ponies, intent on conquering Equestria, and the entire Mario world, but the power of friendship and action commands beat him.
Some cool things that could happen include Luigi helping Fluttershy navigate a ghost house, the ponies wielding power-ups and the Bros wielding magical artifacts (not nessecairly the elements of harmony but some magical artifact), Twilight making an offhand comment about this not being her first time visiting alternate worlds as a reference to Equestria Girls, Fluttershy taking care of a Baby Yoshi, the CMC interacting with the Elite Trio, & of course we gotta have Derpy being her adorable self, possibly riding a Yoshi to deliver mail to the group or some background ponies.
Bowser's dynamic with Tirek would be that they do not really get along well, but they respect eachother.
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I swear we're gonna get these in Antarctica before we get these in Alaska
note: before you ask "What about X" I chose Alaska specifically because I live there.