Shaun is really a sharp sheep. He shows it here in this episode. I never realized how intelligent this sheep was until watching this particular short animated story. Since then, it's become even more obvious.
Because the farmer is in bed with the flu and poor Bitzer is tending to him, the latter can't run the farm. (This episode also makes you appreciate Bitzer more. The dog earns his keep!).
Anyway, Bitzer throws the whistle and day's instructions from the bedroom window down to Shaun, "telling" him - in only language the characters can understand - that he'll have to be in charge today. Shaun thinks that's just tending his fellow sheep but it turns out to be a lot more, such as feeding the pigs, milking the cows, running the tractor, etc.
How he and his fellow handle all this responsibility is pretty funny with non-stop good-and-bad things happening.