Serena, Blair, Nate, Chuck and their class break into the school swimming pool for a night of fun, but when someone nearly dies, the school threatens to expel the person responsible for the break-in. Everyone agrees to not say anything, but this creates major problems between Serena and Dan. Vanessa, while working on a documentary project about private schools, accidentally captures Blair and Chuck discussing their affair. Lily tries to tell Rufus how she really feels about him.

Gossip Girl reports that Serena van der Woodsen was seen buying pregnancy tests. Of course, on the Upper East Side, the truth is often even juicier and more scandalous than the gossip. Nate finds out about Blair and Chuck's affair. And when everyone else finds out what happened Blair's life comes crashing down. Meanwhile, Dan struggles to tell Serena those three special words.

Having been recently dethroned as Queen Bee, Blair returns to school with the support of Serena to find she is still on the outs with her old friends. Dan visits his mother over spring break, and when he returns, Jenny is on the verge of becoming a full-fledged member of the A-List crowd. Jenny must go to dangerous and even illegal lengths to fit in. Serena struggles to adjust to living with Chuck, and receives disturbing packages from an unknown sender.

Serena's world descends into chaos when a former friend, the evil Georgina Sparks returns to town. Nate connects with the last person he expected, Vanessa. Blair hatches a plan to sabotage her biggest rival, Nelly Yuki. Meanwhile Serena goes out with Georgina, but things get so bad that Serena thinks someone spiked her non-alcoholic drink. Jenny develops a crush on a dog-walker, Asher Hornsby, who might be her ticket to permanent popularity.

Georgina informs Serena that she can reveal a deep dark secret from Serena's past, but no one is prepared for what Georgina does next. Blair and Jenny's power struggle continues when each of them start spreading scandalous rumors about each other on Gossip Girl. Dan sees Jenny's new beau, Asher, cheating on her, but Jenny won't listen to him. Rufus goes to Lily for advice on how to handle Jenny's new behavior. Serena tries to confront Georgina, but she leaves before Serena has a chance. After this, Serena says that she and Georgina are not friends.

In the midst of Fashion Week, a furious Blair learns that her mother, Eleanor, at the suggestion of her protege Jenny, has given Serena and her new socialite friend, Poppy Lifton, front row seats to the Eleanor Waldorf show. Hurt once again by Serena's popularity and her mother's betrayal, Blair decides to sabotage the show. Meanwhile, Dan starts hanging out with Chuck, but a walk on the dark side always has its risks and Dan learns that the hard way. Lily learns a secret that her new husband, Bart, has been keeping from her.

Blair sets out on a mission to break up her mother and Cyrus Rose, her new man. Jenny moves in with Agnes as the two continue with their plans for their own fashion line. As Serena continues to fall for Aaron, she learns something that may derail their relationship forever while Dan interviews Bart Bass for an article for New York Magazine.

At the Snowflake dance, Blair and Chuck discover their lookalikes hooking up. Aaron's ex Lexi flirts with Dan, causing trouble with Serena. Nate, Jenny and Vanessa get into a messy love triangle that involves a stolen letter and a revealing dress. Bart Bass suffers a car accident on his way to the ball.

Because Chuck is MIA since his father's funeral, his Uncle Jack arrives on the Upper East Side to find and help him. Trying to forget her last conversation with Chuck, Blair focuses on being accepted into the most prestigious ladies club in the city, Colony Club. Jenny returns to Constance Billard and immediately takes on Penelope and her posse of mean girls, but no one is going down without a valiant Gossip Girl-worthy fight.

Chuck, Jack and Lily come together for the reading of the will which reveals what will come of the Bass empire. Rufus and Lily's relationship is put on hold as Rufus searches for the child he never knew he had. Meanwhile, Dan does some digging of his own and uncovers Rufus and Lily's secret, putting him in an awkward position.

The students are stressed out as they find out who was accepted and who didn't make the cut for early admission to Yale. Meanwhile, Serena bonds with Rachel, her Shakespeare teacher, who is unaware of what Blair has in store for her following receiving her first B; Chuck finds an unlikely ally in his feud with Jack; and Nate and Vanessa have a romantic evening together.

Blair comes up with a devious plan to take down her new teacher, Rachel. Chuck has no recollection of what happened to him when he wakes up in a hotel. Nate and Vanessa try to help Chuck fill in the missing pieces of his night. Meanwhile Dan and Serena try to keep their relationship together as Rufus and Lily grow even closer.

Serena throws Jenny a sixteenth birthday party, but things spin out of control when Poppy Lifton turns the party into the social event of the season. Vanessa agrees to help Chuck in a plan concerning Blair and Nate. Meanwhile, Rufus searches for a way to cover Dan's tuition when he learns he will not receive financial aid to go to Yale.

In a flashback to the 80s, 17-year-old Lily Rhodes gets kicked out of boarding school and runs away to Los Angeles, reconnecting with her parents, Rick and Cece, and sister, Carol. Back in present day, Blair and Nate attend prom together, but the evening doesn't turn out exactly as planned and Chuck and Serena have a little something to do with that. Serena and Lily don't see eye-to-eye over Serena's recent run-in with the law.

Gossip Girl decides to liven things up at the Constance Billard and St. Jude’s graduation by sending out a shocking and damaging email blast in the midst of the commencement ceremony, stirring Serena to come up with a plan of attack. The Mean Girls challenge Jenny to throw her hat in the ring to succeed Blair as Queen Bee next year. Lily and Rufus struggle to repair their relationship after Lily’s betrayal. As for the cliffhangers, Blair and Chuck finally… and Serena is shocked by… and Georgina decides to… and Dan, Nate, and Vanessa unknowingly…. Jenny and Eric do something they might end up regretting.