Wow, triple post already?
Here are some story ideas for every mission in the game:
Reckless Romp: Wario's in his house one day relaxing, while some pesky mice and other creatures try to steal his snacks again. So he's off to go after them, starting this mission of the game. The last boss of it is a giant rat, who's basically the leader of all the rats he's terrorized in Twisted and Game & Wario.
Ogre Attack: While Kat & Ana are going on a stroll through the woods, they run into a band of evil ogres that are kidnapping all the animals in the wilderness. They have to save them and defeat the ogres.
Dash n' Dine: Not much here other than after quite a few training sessions, Mantis proposes to Cricket a new challenge, racing together while eating the most dumplings (and other f00d).
Rhythm Run: After a night of getting down at Club Sugar, Jimmy gets tired and heads back home. But he falls asleep on the way back and when he wakes up, he finds himself in Rhythm Heaven. Now he has to get past every rhythm-action level to get back to Diamond City.
BlasterBlade Power: After heading back from her office job (and seeing her manager Joe off), Mona sees the city being attacked by unknown invaders. She gets an unexpected call, and it's from Penny. She asks Mona to meet her at her lab to get her equipped, giving her a watch that lets her transform into her new battle suit (as pictured earlier in this thread) and her new weapon to take these goons on, the BlasterBlade 8000. (What kind of enemy could it be for this mission?)
Retro Treasure Hunt: 9-Volt and 18-Volt head to the game store to buy the newest action game. They get back home ready to play it together. But once they start it, they get sucked into the TV! They are now in the game itself, and it's all up to them to beat it.
Cosmic Clash: While traveling to more planets throughout the cosmos, Orbulon gets attacked by some notorious space pirates and, yeah pretty straightforward.
The Mighty Taxicapades: It's business as usual for Dribble & Spitz, but they're getting shot at by some enemies.
The Secret of the Missing Spells: When Ashley is trying to find her missing spellbook, she accidentally uncovers a malicious book somewhere in her mansion that unleashes a bunch of monsters who invade it. She has to find all her lost spells (like getting more weapons in a Metroid game) and defeat all the monsters.
Gizmos Galore: Dr. Crygor and Mike are testing their new giant robot, but suddenly, they end up trapped somewhere underneath their lab, and have to find their way around many puzzles with it...? Honestly, I haven't thought a lot about this one in general. Any ideas?
Return to Glory: Wario decides to go treasure hunting on many islands. Who will he encounter on the way there?
What more do you think should be added to these stories? Ideas for end bosses in them?