The world is about to be destroyed by none other than an ordinary human, and the only one who knows about it is an unwillingly chosen fish.

Thanks so much for the advice. I will make some changes to see if it works more. There is definitely and environmental message, do you think it comes across in the logline well/interestingly enough?

If this were my logline, I'd focus more on character 'Fish'. "unwillingly chosen" implies a character of meek traits - just as Nemo was also unwillingly chosen.
Theme feels to be embracing an environmental message: "Man unwittingly destroying earth/sea".

A quick sketch logline for Nemo may read: "When [an overly cautious clown fish], [discovers this son has been captured by deep sea divers], he must [save his son, and escape the dangers of a dentist's fish tank]

"Dentist's fish tank" maybe replaced with "ordinary human destruction" ...