The sequence where Officer Marcus comes into the lair and reads the comic book that Big Daddy had written explaining the history to Hit Girl, the film enters a 3d representation of the comics. (I saw it four times in the cinema.)
This is done with a 3d program; not After Effects. You could do something similar using your favorite The Kid Stays In the Picture recipe (such as this one) only do it with images treated to look like a comic. There are tons of tutorials on how to do comic effects in Photoshop, there were even actions on the Adobe exchange back in the day, probably still there.
There is a Cartoon effect in AE and several other cartoon recipes kicking around the web (again a quick search should turn up a few tutorials.) You would just need your actors to freeze while you were filming. I'm not promising it'll look great, but with proper lighting and planning, you might be able to pull something off.
- The Great Szalam
(The 'Great' stands for 'Not So Great, in fact, Extremely Humble')
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