Here is what I remember:
It was a 90's (I think, not 100% sure, but it's very likely) cartoon series with a rather serious, non-goofy tone about a squad that dealt with paranormal / extraterrestrial activity.
They used a helicopter similar to a Chinook for transportation.
I distinctly remember one episode where a cloud formed over a small town and its rainwater made everyone sick. When the squad made it high up and into the cloud they encountered Octabrain-like creatures that acted as the cloud's bio defense mechanism. I remember those things ate live missiles that were launched at them.
I'm afraid that's pretty much all I remember, aside from the end credits theme being dark and moody.
Hope it rings a bell.