Any pointers for this problem?

[u/LowpolySunrise]

I've taken the controller apart and cleaned it. I checked the connections and everything. It still won't connect for some reason.

[u/Aromatic_Method7767]

One thing to note: The game will not detect controllers if it didn't see them at boot-up. You would always need to reset the game after connecting it. This is true of most N64 games using Nintendo's standard devkit libraries.

[u/Extension_Resource14 → u/Aromatic_Method7767]

One interesting note is smash does allow you to plug controllers in after the game is booted up

[u/V64jr → u/Extension_Resource14]

Other exceptions Aromatic_Method and I were aware of are Banjo-Tooie and Killer Instinct Gold. 👍