Brain uses a machine that can increase or decrease intelligence, and uses it so that Pinky can become smart enough to understand that he is the cause of Brain's failures, due to research Brain conducted. (Brain will later discover he miscalculated his research, and that he himself is the cause of his failures.) Pinky, depressed over the fact that Brain doesn't like him when he is smart, uses the machine to make himself stupid, so Brain will like him again. However, Brain, realizing he has botched his own plans, and believing both of them to be better off with Pinky as the genius and Brain as a moron, uses the machine on himself as well. In the end, both of them are idiots, and thus, are too dumb to operate the machine and restore either of them to their intelligent selves. This is reflected in the episode's final lines.

Pinky: What are we going to do tomorrow night, Brain?
Brain: The same thing we do every night, Pinky.
Pinky: What's that?
Brain: ...I have no idea.
Pinky: Poit.
Brain: Narf.