A scared monster accidentally destroys tokyo and now must rebuild the city while avoiding capture from a crazy zoologist.

There is something shinny in here (but needs work)

It sounds something in between a Manga & Pixar

If you chisel this out for a 3D family film it could work

I am a fan of the original Japanese version of Godzilla and the idea that a monster could accidentally destroy Tokyo felt like a fresh twist on a classic tale. I have two comments that might be helpful. First, in light of the recent nuclear disaster in Tokyo, I am wondering if a story about the accidental destruction of this city might feel a bit intense--however, this may be your intent. Second, I think your logline could be a bit more clear on the main objective of the monster--not getting caught. If the monster is caught he won't be able to rebuild the city. Rough draft of a possible revision idea:

When a scared monster accidentally destroys a major city, it must avoid capture by a ____ (is the scientist crazy if we wants to stop destruction? Maybe this person is just insensitive to the true nature of the monster) scientist so the monster can use its super powers to help rebuild the city.

I'm guessing this is a comedy of sorts? The logline supplies the basic info, I'd like more info about the monster. Otherwise it's hard to picture the movie.