16 year old Joan Girardi is approached by someone claiming to be God. He gives her a mission, get a job. Will Girardi, Joan's dad and new chief of police for Arcadia, is trying to solve the case of a serial killer.

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

God's mysterious ways once again bewilder Joan, when He asks her to volunteer at the high-school art show, so that she can keep Adam Rove's sculpture from being exhibited. Elsewhere, Will feels pressure from the DA's office to call a man a hero after he shoots and kills a home intruder. Meanwhile, Kevin grows weary of receiving special treatment because he uses a wheelchair.

After Joan stands up for one of her classmates being bullied, an embarrassing picture of Joan, taken with a picture phone, is rapidly spread around school. God instructs Joan to join the band. Will must deal with an elderly driver who accidentally killed several people.

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.

As the Girardis are deposed for the lawsuit against them regarding the car accident that disabled Kevin, they look back on their memories of that horrible day.

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.

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.