As summer draws to an end, Blair and Chuck continue to adjust to being in a relationship with one another. Serena returns from Europe with new secrets to hide and a new relationship with Carter Baizen. Nate also returns from vacationing and brings home a mysterious girl, Bree Buckley. Meanwhile, Rufus, Dan and Jenny spend the summer in the Hamptons and learn to adjust to the van der Woodsen's glamorous lifestyle.
Blair, determined to have her Queen status at college, starts her first day at NYU along with Dan and Vanessa. However, Georgina, who was assigned as Blair's roommate, sets out to ensure that she does not retain the Queen status. Serena gets ready to move into her dorm at Brown, but has a fight with Chuck before hand. This leads her to search out Chuck's enemy, Carter, to help her get even with him. Meanwhile, Nate and Bree's relationship continues to grow despite the tension their relationship could cause between their families.
Blair and Chuck face-off when the both set their sights on an item up for bid at Sotheby's. Serena begins to think that Carter may have returned to his old habits, Georgina becomes interested in Dan, and Vanessa thinks that something is wrong with Scott.
During the first day of school at Constance Billard, Jenny takes her place as the new Queen Bee. However, Blair gets in her way. Lily returns home to find that things are not as they were when she left them with Rufus. At NYU, Olivia Burke, an actress, enrolls and is assigned to be Vanessa's roommate.
Lily and Rufus decide to move up their wedding to the next day, but will someone or something come between them before they become man and wife? Chuck discovers a secret that Carter has been keeping from Serena. Dan and Vanessa are pulled into one of Georgina's schemes. Blair is suspect of Bree and shares her concerns with Nate.
Vanessa, hoping to finally win her mother Gabriela's approval, desperately vies with Blair for the honor of delivering the freshman toast at NYU, but at what price? Dan invites Olivia to meet Rufus and Lily, which leads to all sorts of problems for the new couple. Serena and Nate team up to help Carter Baizen.
In need of publicity for his new hotel, Chuck decides to move up his club's opening and enlists Serena's help to get the word out to her celebrity clients. Feeling left out of the planning, Blair attempts to win Chuck's approval by secretly helping him with a problem concerning opening night. Dan is unnerved when he finally watches one of Olivia's infamous sex scenes with co-star and real-life boyfriend at the time, Patrick Robinson. Jenny is forced to choose between her relationship with Eric and her new role as Queen Bee. Rufus gets Lily into the Halloween spirit.
Olivia says something she regrets during her appearance on Jimmy Fallon's talkshow and tries to keep Dan from finding out. With election day around the corner, Nate suspects his grandfather will stop at nothing to get Trip elected to congress. In the midst of another feud with Serena, Blair befriends a new "it" girl and takes her to an election night party at Chuck's hotel, hoping to make Serena jealous.
Not satisfied with just being Queen of Constance Billard, Jenny sets her sights on becoming the Queen of all the Upper East Side by landing the hottest escort for Cotillion. Nate and Chuck plot to help Serena and Blair repair their damaged friendship. Dan is upset when Olivia contemplates leaving school for a movie project.
Hoping to impress the elitist theater kids at NYU, Blair sets her sights on landing a private concert with the hottest musical performer of the year, Lady Gaga. Dan and Olivia sign up to write and star in a school play, based on an idea by Blair and directed by Vanessa. With Blair out of the picture, Serena turns to Nate to help her get through a difficult situation. As a favor to Chuck, Jenny agrees to hang out with Damien, the son of an ambassador who is staying at Chuck's hotel, but the experience proves to be a lot more intriguing than she expected.
It wouldn't be Thanksgiving on the Upper East Side if there wasn't a serving or two of some major drama for the holiday. Blair suspects her mom has been keeping a big secret from her, but it turns out to be something else entirely. Vanessa is supposed to spend Thanksgiving with her parents, but has a fight with her mom and shows up on Dan's doorstep. Rufus learns that Lily has been lying to him about her mother, Cece. Chuck tells Nate that he has some potentially damaging information about one of their friends. Jenny learns that Eric was behind her very public embarrassment at Cotillion and can't pass up a chance to get even. Serena is put in a very awkward position when her mother invites Trip and Maureen to join them for Thanksgiving dinner.
It's been one year since Bart Bass' death, and Chuck must deal with an issue from the past, while news a serious car accident ripples through the Upper East Side. Meanwhile, Dan and Vanessa try to work through their complex friendship; and Jenny is accused of beating up a classmate, which puts Eric in a bad position.
Nate and Serena decide to explore the boundaries of their friendship. Blair suspects that Chuck is having problems forgetting about the woman he saw at his father's grave. Jenny agrees to accompany Damien to a State Dinner but is unaware that he needs her help with a drug exchange. Vanessa and Dan attempt to move past the awkwardness of Dan's confession of love. Rufus returns from a ski trip and tries his best to avoid Lily.
Rufus and Lily grow suspect of Jenny's relationship with Damien. Chuck learns more about the woman who may or may not be his mother. Dan and Vanessa struggle through the awkwardness of dating other people.
Despite being grounded, Jenny continues to see Damien who tells Jenny that he wants to have sex with her. Lily tells Rufus the big secret she has been keeping from him even though she knows it's a huge risk. Dan and Vanessa explore a new stage of their friendship. Chuck is forced to make an extremely difficult decision about his hotel.
Chuck finds himself once again at odds with his uncle, Jack Bass. Eleanor puts Blair in charge of making sure her latest fashion show is a huge success with an important client. Rufus attempts to get Jenny back on track by volunteering to have her help with Eleanor's fashion show, but the opportunity takes a big turn for the worse when Jenny learns that Agnes will be one of the models.
Chuck and Blair are faced with the most difficult decision they have ever faced as a couple. Serena plans a surprise birthday party for Nate, but Jenny does her best to sabotage Serenas's efforts. Dan and Vanessa's new relationship hits a bump in the road.
Chuck offers to throw a wedding for a very pregnant Dorota who insists that she and Vanya have a traditional wedding before her parents arrive from Poland and find their daughter pregnant and without a husband. Dorota asks Blair and Chuck to be part of the ceremony and walk her down the aisle. Serena tells Nate she is having breakfast with the Humphreys when in reality she's secretly meeting up with Carter Baizen. Rufus discovers that Lily has been lying to him about her whereabouts.
When Lily's ex-husband, Dr. William van der Woodsen, shows up unexpectedly in Manhattan, Serena finally gets the reunion she has so desperately wanted with her father, but the circumstances turn out to be far from ideal. When Serena and Nate continue to have relationship issues, a scheming Jenny is more than happy to be a shoulder for Nate to lean on. Meanwhile, Dan finds out that he didn't get accepted into the Tisch writing program and Vanessa admits she may have been somewhat responsible.
Will's return to the Upper East Side continues to stir up problems for Serena, Lily and his long-standing rival, Rufus . Serena and Jenny's relationship is strained as a result of Jenny's deception. Blair spends time on the Columbia campus and realizes where she truly belongs. Dan learns that Vanessa has been keeping yet another secret from him.
When things get tense between Rufus and Will, Serena chooses to stand behind her father, while at the Rufus is made to feel like an outsider in his own family. Meanwhile, Jenny deliberately shares information with Will that may ultimately destroy Lily and Rufus' marriage. After many failed attempts, Chuck makes one last grand gesture to reconcile with Blair, hoping she will finally accept the fact that they are destined to be together.
Blair must decide whether to meet Chuck at the top of the Empire State Building or risk losing their future together. A Gossip Girl gossip bomb involving Dan explodes Serena and Nate's relationship. Dorota and Vanya welcome their baby. Jenny hits rock bottom. Georgina returns to the Upper East Side... and she has an agenda.