It says something when Cate Blanchett (who plays the Big Bad in this film) says it's the most terrifying script she's ever read. The violence is brutal and realistic, with hardly any Gory Discretion Shot. It contrasts jarringly with the dreamy fantasy feel provided by the rest of the film and the Chemical Brothers soundtrack.
Isaacs and his bloodstained canary-yellow tracksuit. Also his creepy leitmotif whistle.
The Container Maze chase scene. Dark, claustrophobic, and eerie. The little pauses in the music and Isaacs' whistling just make it creepier.
Hanna finding Mr. Grimm's body. He has been tortured by Isaacs, who hanged him upside down and riddled him with arrows.
Erik throwing a Mook into the incinerator during his escape from Utrax with baby Hanna.
What Marissa did when ordered to shut down Utrax after Erik stole baby Hanna: kill the other babies by lethal injection, then burn them in the incinerator.