So here's my rough draft. Who knows how much of this will change by the end (if there ever is an end!) Like Anguna, I'm purposely going for a short and cheesy story:
One day, Professor Treeblot was finally putting his finishing touches on Robo-Ninja, his newest invention, a robotic ninja designed to defend the world from Evil Bad Guys. But to his dismay, as he was finishing, the Evil Dr (insert name here) came, kidnapped Prof Treeblot, and scattered all of Robo-Ninja's ability modules throughout the land. Without these modules, Robo-Ninja could do nothing more than run forward. Now Robo-Ninja must travel the land to search for and recover his lost abilities, so that he will be powerful enough to hunt down and defeat Dr (?) and save Professor Treeblot.
So you start the game with the ability to DO NOTHING AT ALL. Robo-Ninja just runs, you can't even control him. Luckily you pretty quickly collide with and equip your first ability module, the "Jump Servos", which let you jump.
And if anyone has cool suggestions for the Evil Dr's name, I'm all ears. I'm shooting for something almost over-the-top silly for his name.
Oh, and my friend Rob just sent me some awesome icons he made for abilities, so that's taken care of. Thanks Rob!