That's another thing. Carl really didn't do anything. He was...just there. He had some friend try to jack Frylock's dying gem and that was it. Sure, the penultimate episode was all about him (and it was disturbing as heck for the wrong reasons at the beginning, but it got better and weirder near the end), but you'd think even he'd have more screen time for the finale. Nope. Not much Carl and no Dr. Weird, Mooninites, Plutonians, M.C. PeePants, not even a nod to Space Ghost (even the movie did that). Just...kinda a let down for a supposed grand finale for a show that took everything to an illogical extreme. And it doesn't even feel like it's a let down as a joke.
And I can't say that something tragic didn't happen to him offscreen. While it doesn't directly imply he's dead of old age, it's easily assumed that's the case. The house seems to be broken down, and Meatwad can't seem to remember Carl's name. I think he even mentions that he used to live there.