Kip and Fiona's marriage is clearly on the rocks due to what happened at the end of the previous season, but the two must work together during the campaign, meaning that Austen and Fiona are unable to continue their fling and can only communicate via Skype. Additionally, the publication of Fiona's book is postponed until after the campaign, allowing Fiona to work with Austen's assistant editor Maxine DeMaine and Jerome in New York to make some changes to the book.
On Austen's suggestion, Kip attends a sexual orientation camp named "Compass". While his progress at the center is at a rocky start, Camilla Bowner, the owner and therapist at the center, helps to speed up his recovery with her sexual treatments. Upon hearing this, and concerned that this may be leading to divorce, Fiona contacts Camilla's husband Trent and schedules a private session with him at her house in Philadelphia so Trent can prepare her for her reunion with Kip once he returns home from "Compass". However, this turns out to be a setup, as Fiona stays in New York as Trent goes to Philadelphia. Kip arrives afterwards and the two wind up having sex. Fiona has caught the sexual encounter on security cameras and tells this to Camilla, who begs Fiona for the tapes, not so she can destroy them, but so that she can display them on a screen above her head so that Trent will open his eyes during sex. Fiona doesn't give in and says she will keep the tapes, as well as stay by her husbands side and not get a divorce. Before signing off, she suggests that if Camilla wants Trent to open his eyes during sex, Camilla should wear a blazer.
After Maxine criticizes Fiona's apparent narcissism in the book and questions her likeability factor, Jerome sends Maxine some new chapters of Fiona's book that reveal some hidden moments of her life, moments which Fiona deems too embarrassing or too boring for herself to reveal. Fiona isn't much impressed with Jerome's fiancee Hayley's attempts to write some new material in Fiona's voice, as she is concerned that she might be perceived as weak in the book, so she goes back to New York to work on the book further. When Maxine compliments Fiona on these changes and mentions Austen's possible reaction, Fiona reveals that Austen hasn't returned any of her calls since the start of the campaign. Maxine is quick to catch on that maybe Austen isn't really attracted to Fiona because he hasn't treated her affectionately. Fiona realizes she may be right and decides to change her book deal and calls Austen to dismiss any possibility of a relationship with him at all, deciding to work on her marriage with Kip. But then Austen changes his romantic behavior towards Fiona, making Fiona feel somewhat better. Upon hearing that Maxine got fired, she checks up on her and finds out that Austen sent her flowers from Scotland and had his nanny (whom Fiona described as an "ancient Scottish woman") meet up with Fiona because he is in love with her, and Maxine used that to get herself fired. Maxine decides to use her retirement package to open up a golf resort for ex-nuns, and wishes Fiona well. Fiona knows well that even though she wants to be with Austen, she still has a few weeks left in her husband's campaign. Instead of deleting the changes, she resolves to keep the changes and keep the character likeable. Soon, Trent returns to Camilla, and they send a donation to Kip and Fiona's home, including a pair of Trent's boxers.
The issue of Kip being gay pops up again when Robin meets up with Fiona, intending to make amends for her sexual behaviour towards Kip. She has gotten help for her depression and realized she had no right to even go after a married man because Fiona would get hurt. Fiona then reveals that during the course of her marriage so far, she has had doubts and suspicions about Kip having an affair, but has come to an understanding over the situation. Robin then reveals that she has taped the entire conversation, and implies she may release it publicly if she cannot overcome the situation any further.
Fiona hires Richard as part of the campaign team, and during a discussion with Kip's campaign manager Ben Tomlund, she recommends Robin as a documentarian to produce video material for the campaign. However, once the hiring transaction is confirmed, Ben reveals he cannot find any sign of Fiona's accreditation, and tells her to temporarily suspend her services until she receives the accreditation notice. So in a moment of desperation, she asks her sister Shevaun Haig, a psychotherapist, to help her get the accreditation. However, Shevaun says that Fiona has to undergo the 50-minute sessions in order for the accreditation to take effect. Fiona also learns from these sessions that her own mother isn't doing so well. Fiona feels run-down during the sessions with Shevaun because she reminded her of everything that went wrong in her life, and starts to feel that her own sister is using her for her own benefit. When Shevaun signs the accreditation form, Fiona feels relieved, and as a result, her popularity as a web therapist starts to skyrocket as a result.
Fiona begins to gain interest from high-profile celebrities such as Kirsten Noble, who interviews her for her popular blog "Neuroticornucorpia", and television actress Allegra Faverau, who found Fiona's book on a plane, and wants to film a movie adaptation of the book with herself starring as Fiona for Lifetime. However, Kirsten puts some weird sexual fantasies featuring a persona known as "Filona W." and some digitally altered photos of Fiona on her blog, which does not do good for the campaign, and makes Kip suspect that Fiona is a lesbian. However, after lawyer trouble, Kirsten censors these fantasies and puts a link on her blog to Web Therapy, and both do admit that it has attracted wild publicity for both of them; TMZ picked up on the blog and the LBGT community is giving their support to the campaign. However, after Fiona agrees to appear on a live chat on Kirsten's blog, they both discover that her blog is inaccessible. Fiona then realizes that Austen had bought BlogSpot, the domain which Kirsten's blog is under, and the blog may have been erased in the acquisition. As for Allegra, Fiona accompanies her to Los Angeles to prepare for her role, but Jerome asks Hayley to accompany her on the trip. The trip does not go well, when Hayley is arrested at the airport due to mysterious scissors in her luggage, and Fiona encourages Allegra to have a drink, and unknowingly and unwittingly causes her drinking to go out of control. Allegra believes her career to be over, but Fiona reveals that Lifetime are moving forward with the movie project, just not with her.
Fiona then encounters Gina, who, after losing her job, is finding it difficult to adjust to being unemployed. Fiona tries to help her find a good job, but doubting that she can work herself at such a low level as a receptionist, she tells Gina that there is a job opening in Yukon Canneries in Alaska as a shipping specialist. Some time later, Austen promotes her and she prepares for her new job in London.
Jerome and Hayley have married and are trying to have a baby, and have hired a surrogate Tammy. Fiona soon learns that Tammy is expecting Jerome and Hayley to do favors for her and give her large cheques, and risks jeopardizing Jerome's position in his job as a result. After some negotiation with Tammy, she agrees to give Jerome a raise to cover the expenses. However, she realizes that Tammy is lying about the pregnancy and scamming both Jerome and Hayley, and informs Jerome about her deception. Jerome is grateful that Fiona saved his marriage from a con artist, and now he and Hayley are starting to talk about having a family the right way.
Fiona becomes angry when she discovers that Ben has postponed her appearance on a TV show and indirectly accuses her of making Kip lose his youth and damaging his career. She starts to suspect a relationship between Kip and Ben beginning. Upset about this accusation, Ben almost quits the campaign. However, they resolve their differences and agree to work together for the campaign, and Ben assures Fiona that there is nothing going on between him and Kip.
Fiona does a series of video chat sessions with her college friend Newell Miller, whom she does not recognise at first. After he attempts to break into her home, he reminds Fiona that she slept with his father, a professor, at one point while they were in college, and Newell witnessed the sexual encounter. As a result, he has had a series of disastrous relationships because the women remind him of Fiona. He plans a romantic session with Fiona to cure himself of his obsession, but Fiona turns him down, not willing to cheat on her husband during the campaign. She does set him up with some sessions with Shevaun, which helps to finally cure him. When quizzed on how she knows Shevaun, she tells Newell of their family history, and that she went to the same college as Newell because Shevaun went there before. Shevaun may have inspired her to sleep with the professor when her grades were plummeting, a trick she might have done earlier, when her hair was blonde. Newell is unsure whether or not he may have witnessed Shevaun instead of Fiona on that day, but he knows that Shevaun definitely started it.
Fiona discovers that Putsy is in danger of being charged for the murder of her roommate, which may have been the result of her puppetry practice. Fiona succeeds in helping her mother avoid the murder charges. However, she is horrified when she discovers that she is starting a "Net Therapy" business and using puppetry in her practice.
In one of the final storylines of the season, Fiona discovers that Richard has feelings for co-worker Robin, and has started dating her. Another session with Richard and Robin reveals that Robin ordinarily doesn't get serious with co-workers at all. Richard isn't surprised, but thought she had real feelings for him, and Robin reveals she is dating him as a rebound after her relationship with Kip. She reveals she possesses tapes which apparently show Kip and Ben engaging in sexual intercourse, infuriating both Richard and Fiona. Fiona demands that Robin hand over the tapes, but she refuses despite the terms on her contract. She implies that Richard is only dating her to move on from Fiona despite the fact that he is still in love with her, which he denies. Fiona also starts to see how condescending Robin is to Richard, and how he is becoming more and more upset by her, and it reminds her of how her chances of a possible romance with Austen are being hindered by her husband's campaign. Unable to take it anymore, Fiona fires Robin and Richard breaks up with her, and Robin does what Fiona had expected; she releases the tapes and puts the entire campaign in jeopardy. Kip starts to panic and then eventually resigns from his candidate post. Fiona is horrified to see that the viral video editing the resignation to make it appear that Kip is "coming out" is getting more attention than the actual resignation.
Kip's downfall does not stop Fiona from achieving her own success in her rights, as Hayley asks Fiona for her forgiveness for the sessions and the airport incident, which Fiona accepts, and announces with Jerome that they helped with the Lifetime movie project. Hayley had pitched the movie to be reworked into a musical named "Whistlin'", which was very popular with the network. Despite the fact that the format is now different from Fiona and Allegra's original plan, Jerome convinces her that the characters will be explored further using this format and she reluctantly agrees to let them work the project as long as she receives royalties for being the author of the book that originated the movie. To accommodate the new production schedule, Jerome decides to temporarily work for Putsy for her "Net Therapy" business, and has Hayley take his place as Fiona's assistant. Fiona objects to this new arrangement, so Hayley says that if that doesn't work, she will do another Lifetime project along with the movie, about a man who is trapped between his lover, his partner, his supporter and his boss. Fiona, mostly because it doesn't matter because she needs to talk to Austen and may be going to New York for a while, feels more than happy to let them do whatever they please, and Jerome and Hayley are surprised to finally see some good heart from the therapist.
Kip tells Fiona that he is going to Sante Fe, New Mexico with Ben for a while, because they need some time apart and he ultimately needs to know what he wants to do next. Despite their impending separation, they decide to keep good memories of their time together and wish each other well. Later, Fiona announces her separation to Austen and tells him that now they can be together. When Austen appears to be worried, Fiona assures him that they can take things slow because she isn't divorcing Kip yet. However, Gina comes onto the video screen, saying that she took four pregnancy tests, all positive, and tells Austen that they are having quadruplets. She then realises that Fiona was watching her at this moment. Austen assures Fiona "It's not how it looks." as she stares in shock on the fact that her best friend may be pregnant with her potential lover's child. A confused Gina says the final words of the season: "How does it look?"Lisa Kudrow as Fiona Wallice (11 episodes)
In December 2011, Showtime renewed Web Therapy for a second season of 11 episodes, premiered on July 2, 2012. Guest stars for season two include, Meryl Streep, Conan O'Brien, Rosie O'Donnell, Julia Louis-Dreyfus, Molly Shannon, Minnie Driver, and Selma Blair. David Schwimmer is set to appear in a four-episode arc as Newell Miller, a man who tracks down Fiona for help after a past experience which she was involved in, has affected his love life. Episodes ten and eleven of season two will air on Sunday at 10:30pm following Weeds, instead of the usual Monday at 11pm time slot.