I used to teach English, so I'm quite capable of catching grammar and punctuation, as well as style.
What I'd normally do is take the story in DOC format and mark corrections with red text, along with commentaries and suggestions.

I have a speech engine that makes the computer read the story out loud. You won't believe how many errors that catches!
I also taught English for 4 years at a local school, including grammar, punctuation, literature, composition, and vocabulary, so I know what I'm talking about.

Though I have a slight case of dysgraphia, thus requiring several correction passes for my OWN fanfics in order to get them right, which includes the speech engine mentioned.

Right now I'll start with Kids Next Door, Hey Arnold, and Tiny Toons Adventures. I'll try to do a bit of Jimmy Neutron as well.

Please, NO ANIME, no Script formats, and if your story is a cross-over, let me know what shows are involved because I'm may not be familiar with them.
You'll also note I included all ratings, but the higher ones must have literary merit and not just have gratuitous content.

Cartoon Care Bears Cartoon Chip and Dale's Rescue Rangers

Cartoon Codename: Kids Next Door Cartoon Hey Arnold

Cartoon Jimmy Neutron Cartoon My Little Pony

Cartoon Tiny Toon Adventures

General Romance Humor Drama Adventure

Mystery Horror Angst Supernatural Suspense

Sci-Fi Fantasy Spiritual Tragedy Crime

Family Hurt/Comfort Friendship