Below is a draft of the story. I kinda visualize it as a storyboarding for some cinematics of a game, so I will wrote it with that in mind. Hope to develop the storyboarding too.

"This is 'Ben'. As many juvenile monsters of his species, Ben is very adventurous and will always try to go beyond the boundaries of its natural habitat.
One day Ben went so far that he got lost. Trying to find his way back just got him even more lost and now a storm was approaching.
Luckly, Ben found the entrance to a cave in a very weird looking mountain area. Without further delay, Ben rushed into the cave.
It should not be a problem for him, because Ben has infra-red vision and a good sense of smell, so wandering in the darkness is something he is supposed to be good at.
The problem is that Ben is a very clumsy monster, and deep inside the cave, he ends up putting himself in danger. He trips, falls, rolls down a slope, bump into several stones, injuries his arms and legs, and ends up crashing onto a wall. Poor Ben... He faints, and only wake up some time later. He decides to climb back. Its not raining anymore. Injured, Ben tries to find his way back home again...
After an hour of walking, Ben starts to feel unwell. His body is getting hot, his body is aching, legs getting tired...
Yup... Ben is sick... He probably was infected with all sorts of viruses, bacteria and other microorganisms that inhabited the strange environment of the cave. He got it through his wounds...
With no stamina, Ben stops to rest.
But he need not to worry, because for a monster as he is, Ben's body is equipped with a kick-ass immune system that will deal with the infection. Inside his body, Ben has special antibodies that are as monstruous as him. These creature-like proteins will get rid of those &#@%# microorganisms and fix Ben's body in the blink of an eye."

So... here is where the adventure is supposed to start. The Nanomonsters are the antibodies and they will have to go in a molecular journey to fight against the several "things" that infected Ben. But of course, some things will happen along the way and the journey will be more difficult than it appears to be.