Sixteen-year-old Joan Girardi and her family have recently moved to the town of Arcadia, Maryland. One day, she encounters a boy of about her own age who makes an extremely outrageous claim: that he is God. He gives her a simple assignment: get a job. Meanwhile, her father, Will Girardi, is investigating a serial killer.
For her second assignment, God tells Joan to enroll in the advance placement chemistry class. Meanwhile, Will runs into difficulty, particularly from the obstinate district attorney, during an arson investigation.
Joan is told by God to learn to play chess while the very sceptical Will is forced to work with a psychic in order to find a kidnapped toddler. His more mystical wife is hoping at the same time that a miracle will happen to Kevin.
Given her recent odd conduct, Helen fears that Joan may be beginning to be eccentric and lose touch with reality. Meanwhile, Will tries to repair his strained relationship with Kevin and, at the same times, improve his disabled son's quality of life.
God instructs Joan to hold a garage sale the following Saturday. While rummaging through her family's old belongings, she finds painting created by her mother during a difficult time in her life. Joan also attracts the attention of another student. Meanwhile, Will fights desperately to bring a rape case to court despite the fact that the district attorney feels there is insufficient evidence. Kevin finds a newspaper job.
When God instructs Joan to try out for a position in the cheerleading squad, she learns the difference between friendship and popularity. Joan's lesson occurs against the backdrop of an investigation into an infant abandoned in a dumpster. The evidence points to an Arcadia High School student. Meanwhile, Friedman begins to think his best friend, Luke, is gay.
Joan babysits Rocky, a six-year-old boy who has a morbid fascination with death which she finds disturbing. Meanwhile, the Arcadia Police Department is faced with controversary by the assault of an unarmed black man by two white officers.
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.
God wants Joan to score an "A" on a test about French saint Joan of Arc. As the teen hits the books, she draws comparisons to the life of the young heroine who claimed to hear divine voices and was burnt at the stake. Helen finds her daughter's newest obsession troublesome and urges Will to have the entire family visit a therapist. Meanwhile, Will is unjustly raked over the coals for shutting down a crack house.
Each of the Girardis deal with crises of varying seriousness, the worst of which puts Will at the mercy of a crazed gunman. The day also finds Helen reacting with mixed emotions after getting a positive result on a home-pregnancy test. Meanwhile, Joan dreads having to take her driver's exam, and Luke is presented with a major distraction just before he's supposed to compete in a high-stakes competition.
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.
Joan is saddened when she learns Rocky has passed away, causing her to further question God about life and death. Will loses his job when his discovery, and whistle blowing, of a political conspiracy causes the town government, and police department, to be desolved. While Luke continues to work on his science project and his growing attraction to Grace and Kevin is injured in a game of basketball.
At Helen's insistance, she and Will take a getaway to a spa, but all does not go well when Will cannot forget about his job. And with the parents away, the kids are up to a little recreation of their own; Kevin and his boss, Rebecca, find it hard to ignore their mutual attraction; Joan, as she is trying to sort out her feelings for Adam, is instructed by God to throw a party while her parents are away; Luke helps Joan pull off a successful party.
God tells Joan to join the debate team, where her partner has a stuttering problem. A new security system is implemented at Arcadia High School. After the art teacher quits, Helen wonders if she would be right for the job. Both Kevin and Luke seperately deal with the aftermath of a kiss. And Will and Toni deal with a case involving a reverend accussed of child molestation.
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.
God tells Joan to learn to jump rope with a group of inner-city teens, one of whom Joan discovers is homeless. Kevin goes on a date, but not with who you think.
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.
God instructs Joan to help out with the a chaotic Girardi household; Adam has his first art show; Will and Toni witness a carjacking. Will and Toni, while making an arrest, get stuck in an elevator with a pregnant woman who is about to give birth; Kevin believes he might be recovering some sensation in his stomach area and gets an EMG (a nerve conduction) test done.
God tells Joan to take piano lessons; Joan helps her piano teacher deal with her past; Joan learns a painful secret Will and Helen have been keeping from the family; Iris becomes suspicious of Adam and Joan closeness.
Feeling threatened that Iris and Adam continue to share a bond over their passion for art, Joan vows to discover a hidden talent that Adam will admire. However, her disastrous attempt to be the yearbook's star photographer soon adds to her insecurities about losing him. Meanwhile, Will and Toni attempt to set up a sting for a man who is planning to hire a hitman to murder his wife.
Joan takes a cosmetics class, per God's request, and Kevin doesn't react well to crossing paths with the last girlfriend he dated before his disabling accident. Glynis' flattering makeover attracts a great deal of positive attention at school, which only adds to Joan's disappointment when Adam fails to notice her own new look. Meanwhile, Kevin, who remains bitter with the belief that he had been dumped by Beth because he had become a paraplegic, harshly rebuffs her efforts to make peace with him.
After God tells Joan to give Adam a gift, she finds something that leads her to wonder if God's suggesting she have sex with him. While secretly searching through Adam's backpack for gift ideas, Joan is stunned to find a condom there. She soon wonders if sex is the "gift" God had in mind, and she nervously ponders whether or not she'd be ready for such a big step. Meanwhile, Kevin begins covering court proceedings for the paper and ends up causing a stir in one of Will's cases.
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.
God instructs Joan to start a community garden; Judith continues her downward spiral; Luke puts up a strong front with Grace; a former police informant is killed setting Will and Carlisle on a mission to find corrupt cops.
God has Joan adopt a wild cat; Helen's Aunt Olive has a stroke while visiting; Will calls Internal Affairs to investigate for corrupt cops.
Things get dirty in a student council election as God instructs Joan to support a candidate; Helen must deal with a student who protests another students work of art.
God tells Joan to help her mother collect clothes for the homeless; Kevin attempts stand-up comedy in order to impress Beth; Will wants to counter-sue the Bakers.
Joan struggles with the pressures of Junior year; God assigns Joan to work on a videography; Adam and Judith work on a project together; Will, Kevin, and Helen meet with a lawyer to discuss a counter-lawsuit.
After being prodded by Judith to go on a real date, Joan and Adam nervously prepare for a romantic night at a fancy French restaurant. Little do they know that Judith has subsequently made some misguided plans for herself for that evening, which later causes the guilt-ridden Joan to wonder if she could have prevented her friend's misfortune.
As Joan begins to deal with Judith's death, she faces the added pressure of having to relive the day of Kevin's accident during her deposition. Meanwhile, Will feels guilty as he recalls how poorly he treated Kevin in the hours preceding his accident. Additionally, Grace reluctantly agrees to join Luke for dinner at the Girardi's on his birthday.
While helping Grace shop for a dress for the occasion, Joan is delighted to finally meet Grace's seemingly perfect mother, Sarah. However, when Sarah's drinking problem becomes evident, Joan begins to understand why Grace is so private – and why she's long been avoiding having her bat mitzvah. Meanwhile, Luke racks his brain to come up with a meaningful bat mitzvah gift for Grace. Additionally, Adam and Joan have different ways of coping with Judith's death. Will supports Lucy's less-than-legal means of trying to get one of Judith's friends to describe Judith's on-the-run killer, and Kevin's ex-girlfriend is deposed for the trial.
As Joan tries to work her way up to the high dive despite her acrophobia, Luke attempts to overcome his paralyzing fear of undertaking an activity at which he might fail. Meanwhile, Will continues his quest to find Judith's killer, and Kevin goes on a date with Beth. Additionally, while reflecting on Judith's death and Kevin's accident, Helen becomes overwhelmed with concern about her family being in harm's way.
Despite everyone's protests, Joan allows her snobby, Ivy League-educated guidance counselor to advise her against applying to college. However, after Joan relays her plans to Roger, an engaging college student on the campus she's visiting, he tells her that college is attainable and persuades her to hire him as a tutor. Meanwhile, Adam becomes jealous of Joan's rapport with Roger; Will sees a dark side of Lucy; Helen questions her commitment to Catholicism, and Beth finds it difficult to resume a relationship with the wheelchair-bound Kevin.
God instructs Joan to try out for the school play; Adam builds the sets for the play; Grace becomes jealous of Luke and Glynis.
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 wants Joan to do an extra credit assignment on Romantic poetry; Adam takes on a perky and cute assistant (special guest star Haylie Duff); Lucy gets a promotion; Helen takes a break from her Catholic studies; Kevin decides to get back into the dating game.
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 is convinced that she's meant to help Stevie keep her part-time job with Adam, despite Stevie's mother's order that she quit. In an effort to supply Stevie with the Social Security number that Stevie's mother is withholding, Joan gets Kevin to use his investigative reporting skills. Kevin's findings end up leading Will to make a discovery that quickly turns Stevie's world upside-down. Meanwhile, Adam is upset with Joan for telling Helen that he tried to have sex with her, and Kevin is conflicted when the local television station asks him to do a report that pertains to paralysis.
After Price discovers Joan holding an empty egg carton near his freshly egged car, he wrongly assumes she's the culprit and punishes her with a weekend of community service. Without more direction from God than to rise above the injustice, Joan tries to figure out if she's meant to help a bitter former nun, Lilly, who is overseeing the service project, or one of the social outcasts who are serving as a result of their own offenses. Meanwhile, Joan's also upset that her reluctance to begin a sexual relationship with Adam is driving a wedge between them. In the meantime, Adam meets a troubled artist at the community center; Joan gets Luke a job at the bookstore; Kevin has another car accident.
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.
In the wake of Joan's difficult breakup with Adam, God tells her to do some therapeutic cleaning, which ends up putting her in the middle of a scandal involving her guidance counselor. As part of Joan's clean sweep, she returns everything Adam ever gave her, which only adds to the awkwardness between them. Meanwhile, when Joan returns some items to Mr. Tuchman that he loaned her, a jealous student with feelings for Tuchman vindictively tells the school authorities that Tuchman initiated intimate relationships with both her and Joan. In the meantime, Kevin considers getting a place of his own.
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.
God tells Joan that her last two years were just practice for her greatest challenge, which will be to face off against a mysterious man who, though he also talks to God, has a sinister agenda. Initially, Joan is simply curious about Ryan Hunter, the charming, wealthy and influential man who revealed to her that he also speaks to God, and who rescued Adam from the woods during a storm. However, she soon discovers Ryan's dark side and is alarmed that he's insinuated himself into the lives of her loved ones, who are quick to dismiss Joan's qualms about him.