Joan enrolls in advanced-placement chemistry, after God asks her to stop being an underachiever; Will ruffles feathers during an arson investigation.

Joan baby-sits for a 6-year-old boy who is obsessed with death; officers assault a black man at a gas station.

Joan's newest mission from God is to work with kids, so she volunteers to help babysit children of abused mothers; Joan becomes jealous when Adam falls for one of the volunteers; Kevin starts to get cocky again and sleeps with his girlfriend, Rebecca; previous events emotionally catch up with Will; and Luke makes a shocking admission to Kevin.

When the hospitalized Joan is diagnosed with Lyme disease, she begins to question if she's been seeing God or merely experiencing the hallucinations that can be symptomatic of her condition...

Upon hearing that Joan may have been suffering from the symptoms of Lyme Disease for months, a somewhat relieved Will and Helen believe this news may explain Joan's mood swings and atypical behavior, while a concerned Adam wonders if Joan will be different upon her recovery. Meanwhile, the hospitalized Joan experiences a crisis of faith -- and considers revealing to someone close to her that she's been talking to God. In separate circumstances, Helen and Will begin to rethink their belief systems after, respectively, experiencing spiritual dreams and miraculous events.

After a summer of therapy and with school resuming Joan tries to return to a ""normal"" life even as she ignores God, who keeps reappearing; Will is sued for emotional distress by Andy Baker, whose drunk driving caused the accident that paralyzed Kevin; Luke and Grace try to adjust to their relationship.

After saving a girl's life Joan suddenly becomes famous but she soon learns fame is fleeting and can even turn against you; Adam has a job interview that doesn't quite go the way he wants; tension builds between Lucy and Will; as Luke prepares to get his drivers license Grace tries to educate him on the harmful impact vehicles have on the enviroment.

God tells Joan to do an extra credit English assignment on romance poets, which causes her to question her own love life.

God tells Joan that the last two years were a spiritual boot camp for her greatest challenge yet, pitting her against a man with a sinister agenda.