Helen fears Joan is becoming eccentric when she enthusiastically tackles her boat-building project; Will encourages Kevin to join a wheelchair basketball team.

God instructs Joan to ask a troublemaker to the winter formal. Will uncovers secrets that could prove unfavorable to the former Chief of Police and other members of the city's government.

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.

Judith, a wild friend of Joan's from summer camp, starts school at Arcadia High; Will investigates a drive-by shooting; Kevin confronts Andy about the on-going lawsuit.

Incensed that Will and Helen have forbidden her to go to a concert with Adam and stay overnight with him in his father's camper, Joan goes anyway.

After Joan has a conversation with God about free will, she decides to use it as a rationale for lying to her mother in order to go on the trip as she's convinced that Helen simply wants her to remain a dependent little girl. Meanwhile, Luke is shocked when the nerdy, girl-obsessed Friedman rebuffs the advances of the surprisingly infatuated Stevie.

Joan prepares to prosecute a case for a mock trial at school, per God's request, while enthusiastically planning a way to celebrate her one-year anniversary with Adam, who has secretly betrayed her.

Joan surprises everyone with her passion in prosecuting a mock case against the equally motivated defense attorney, Grace. Meanwhile, while trying to hide his guilt from Joan as she plans a special anniversary night out with him, Adam decides to confess his wrongdoing to an appalled Grace.

Meanwhile, Will investigates the murder of an eight-year-old girl and Helen continues her study of catholicism.

Joan and Grace fear the worst when, on the heels of failed attempts to reconnect with Joan, the emotionally fragile Adam goes missing during a hike...

Despite Grace's attempts to foster a more comfortable rapport between her friends, Joan is intent on hurting Adam with her rebuffs, which she regrets when it appears that his life may be in danger. Meanwhile, Helen is shocked when a priest tells her that the man who raped her 25 years ago would like her to visit his deathbed so he may apologize. Also, Luke is dismayed and intrigued when he learns that Friedman has been getting stoned.