Perhaps the episode where he and Sue Ellen do that dinosaur project together, but Brain tries to insist on doing the work himself, fearing that any of Sue Ellen's contributions would be too girly, and cost him a perfect grade?That said, back to the show... can anyone pinpoint the exact moment where Brain started becoming Brainy Smurf? I know the Kafka's Metamorphoses parody Pest episode was a key point in that... but I can't help that it started earlier.
But one thing that stands out in my mind now is when he introduced the show by talking about the difference between day and night because of the earth's rotation, then Arthur interrupts him saying they don't even know what he's talking about, but Brain says they're smarter than he thinks... then looks straight at the audience and says in a baby tone, "Would you lke to learn about gravity?" and it turns out he was talking to Kate and Pal.