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Question

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.

Answer 1

Sci-Fi with a teen/Young adult jumping all over the place with a simplified, but notable art style? could be Martin Mystery, in some episodes: where as usually colorful, as seen below, Martin would where a black turtleneck under his colorful shirt when going into colder climates:

The general tone of the Sci-Fi based show was Spooky comedy. Could this be what you are looking for?

Answer 2

Could it be "Real adventures of Johnny Quest"

Answer 3

Could it be Pirates of Dark Water?