Okay, so there is a secret organization that investigates incidents with aliens.

Am I describing The X-Files, Men In Black, or UltraSeven X?

Okay, so said organizations have members named Agent K and Agent J. K knows more about the organization and aliens, while J is more of a newbie. Together they fight aliens that pose a threat to the Eart.

Men in Black or UltraSeven X? 

Okay so Agent J has the ability to turn in UltraSeven and the show is super Big Brother-ish. Led by the Shadow People.

Yeah, UltraSeven X is a fusion of Men in Black, X-Files, and Ultraman. 

I got into this show as well, but it only has twelve episodes and was released in 2007. And yes, only now is it being released in the US.... for only five days. :/

But at least it's on Youtube......