I used to watch a cartoon when I was a kid, sometime during the the 2000s(?).
I remember that the story was pretty dark, or mystery related. The art style was something like Batman: The Animated Series. The protaganist was a boy, probably a teen or a guy in his early twenties at max. He had blonde hair, and usually was dressed in black clothes. I don't remember any details of the story, except that there was an organization/group of people chasing him for some reason.
I remember a scene in particular: the protagonist into some kind of mall/research building, jumping from the second floor with some kind of skylight above him, while shooting.