This is one of the very few times Ned Flanders had a villianous role. He banned the theory of Evolution and Lisa was arrested for teaching it. However, he apologizes to Lisa for what he did and even offered to take her and the other kids out for ice cream.
This is the second time in the series that only Lisa was arrested. However, she's not shown in jail implying she was droped off at the Simpsons house.
From this episode onwards, Ned develops a greater respect for religions outside of Christianity.