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 God suggests she be part of a growth process, Joan decides her science project will be to plant a garden in an inhospitable area to see if it can survive.

Gods 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.

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

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.

Also, 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 breakup with Adam, God tells her to do some house cleaning, which puts her in the middle of a school scandal.

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.