While people might remember it fondly, in reality, CatDog was a creepy show. It was one of the most bizarre '90s cartoons ever created and considering the existence of Rocko's Modern Life, that's saying something. Some of the reasons that CatDog was super weird are inherent in the concept - a cat and a dog attached at the stomach is unnatural even before you start thinking about the implications. Those implications are pretty terrifying, though. For example, how do the siblings go to the bathroom? No one knows for sure but there's no possible explanation that isn't horrific.
When re-watching any old episodes from this show, further weird details emerge. Another odd fact, Cat and Dog's sarcastic roommate, Winslow, actually raised them from childhood. If that doesn't sound strange, then you're not remembering all the episodes when Winslow and Cat actively tried to murder each other. Oh, and there's also an episode when Dog hallucinates that raw meat is talking to him. He ends up trying to cook and eat Cat. You probably won't find that episode in any Nickelodeon fan art.
Cat and Dog spend a disturbing amount of time just hanging out inside each other's mouths. In one iconic clip, Winslow walks in on the two of them standing in their room while Cat is rooting around inside Dog's mouth. In another much more terrifying scene, Cat crawls through their body, leaves his skin behind, and comes out through Dog's mouth as a horrifying skinless monster.
He does this in order to forcibly brush Dog's teeth.
Some episodes of CatDog are more disturbing than others. "Meat, Dog's Friends" is one of the worst. In this episode, Dog realizes for the first time that meat comes from animals. This is a shocking realization for many five-year-old humans but Dog is supposed to be an adult. He reacts by deciding to become a vegetarian. Cat thinks that it's terrible idea, though, because dogs are obligate carnivores.
Dog has a nightmarish hallucination in which the ghosts of meat-based food he's eaten appears and explains how he killed them. As the episode unfolds, everything from vegetables to rocks tell him that they're friends, not food. Eventually, Dog goes completely off the deep end and tries to eat Cat, since Cat is his brother not a friend. After a terrifying sequence when Dog snaps, growls, and tries to cook his sibling, the whole thing is resolved.
They find out that meat grows on trees so it's totally okay to eat.
One of the biggest CatDog mysteries is how they go to the bathroom. People have come up with plenty of theories and all of them are terrible. One involves excreting waste through each other's mouths in a reverse centipede sort of situation. One involves their excrement being teleported to another dimension and one involves having separate anuses and most likely, separate penises as well.
Creator of the characters Peter Hannan says about their situation:
"No one knows [how they relieve themselves], myself included. What I used to say, because I was worried that kids might think CatDog would explode if they didn't go to the bathroom, was that they definitely do go to the bathroom, but no one knows how. Nobody ever asks how Mickey Mouse goes to the bathroom, so we don't really need to know."
Mickey Mouse presumably has the parts required for the process, though. We don't see them because he's wearing pants. He doesn't have another animal's head attached to his rear end. So it's probably a different sort of situation.
In episode "CatDog's End" (which is not the last episode), Cat decides that he's sick of living the conjoined life he wants a separating surgery. The process is, apparently, easier than buying a used car; he just walks into the Better Bottoms store, picks out a new rear end, and schedules the surgery. No one ever mentions that it's incredibly difficult for adults with multiple combined body parts to safely part.
Ultimately, Cat and Dog decide not to do it because they want to stay together and because the would be surgery tool is a rusty looking blade that's powered by bicycle pedaling.
Only Rancid Rabbit, another odd character, seems to enjoy the pain of swapping out his lower half. He's had the surgery 14 times.