Season Two begins with Chuck's quest to try and win back his "true love", Blair Waldorf in the season premiere "Summer, Kind of Wonderful". Blair, however, reeling from the fact that he ditched her at the airport, has hooked up with a handsome, seemingly perfect Georgetown guy by the name of James, originally in an attempt to make Chuck jealous. Even though he immediately sees through her ruse, he is crushed when he spots Blair's heart pin on James's sleeve, and she succeeds. Chuck is suspicious of James and orders a background check on him.
At the posh White Party, Blair makes out with James in a blatant attempt to provoke Chuck, but James finally catches on and is devastated that he was being used. She admits that he bores her, but they later reconcile when James admits that his name is actually Marcus and he is a British lord, just as Chuck gets a call with this same information. Dazzled by this revelation, she decides to carry on their relationship, but Chuck tries to stop her and admits that the reason he abandoned her was out of the fear that she would see "him," implying that he was afraid to let her get too close. However, when Blair asks him to tell her that he loves her "Three Words.Eight letters.Just Say It", Chuck is unable to say the words. Blair, obviously disappointed, decides to leave with Lord Marcus. Chuck, who is still very much in love with Blair regrets the mistakes he made and drowns his sorrows in alcohol.
Chuck again tries to sabotage their relationship, this time by introducing Marcus's disapproving mother to Blair. Over breakfast in the Hamptons, he becomes buddies with an unsuspecting Marcus and later gets him to reveal that his stepmother, Catherine, tends to drive the women in his life away. Chuck attempts to exploit this by bringing Duchess Beaton, who turns out to be Catherine, Nate's cougar, to one of Blair's parties. His plan to have Catherine drive her off fails when Blair discovers her and Nate Archibald in a passionate embrace and is, thus, able to blackmail her into accepting their relationship. During this episode, it is also revealed that Chuck has sold his share of Victrola after secretly agreeing to loan money to Nate's mother since they are having money trouble. Nate is outraged when he finds out, despite Chuck's good intentions, but quickly forgives him by episode 3.
In Episode 3, "The Dark Night", it is revealed that Chuck is suffering from impotency because of his lack of intimacy with Blair. He attempts to distract himself many times with a number of women, but finds himself physically incapable of sleeping with them. When Serena tells him it is likely he is not over Blair, he decides to try seducing her one last time so he can move on. During her back-to-school party, he gets her to admit that Marcus and her haven't been having a physically satisfying relationship. He tries seducing her, but fails the first time. Eventually, he successfully lures Blair into a heated kiss during the citywide blackout, but Marcus walks in on them when the light is restored. She is visibly distraught when they are caught together and runs after Marcus, much to
Chuck's displeasure. Later in the episode, he once again tries hooking up with another girl but cannot, forcing him to realize it's because he wants Blair, and only Blair
In Episode 4, "The Ex-files", Chuck continues his pursuit of Blair in a very Machiavellian fashion. While the episode was heavily focused on the awkward break-up of Dan Humphrey and Serena van der Woodsen, it is revealed that the majority of the post-break-up awkwardness was all due to Chuck. By hiring a girl named Amanda to act like she was interested in Dan, he caused Serena’s jealousy to flair, and regress to her former “bad girl” ways. This causes her to reclaim her former status as Queen Bee right out from underneath Queen Blair's nose. Meanwhile, Blair is busy finishing off all relations with Marcus (who she found out was cheating on her with his Catherine) and is bewildered when she returns to find that Serena has become the new “Queen,” dethroning her best friend.
Chuck reveals that he was the mastermind behind Serena's return to power and did so in order for Blair to take him back as an ally in the war against Serena. However, Blair essentially ignores Chuck’s offer and insults him by telling him he could never act like a human being, while also pointing out his lack of friends.
Chuck agrees to let Dan Humphrey hang around him for an evening out of boredom, not knowing that Dan plans to use him to write a story. Later, Dan finds out that Chuck is actually love-starved for his father's attention after he witnesses a failed attempt of Chuck setting up a meeting with his father over the phone. The two then bond after Dan later stands up for him during a bar fight, and they wind up in a jail cell together where Chuck becomes soft for a moment and opens up to Dan about his father. Chuck believes his father hates him because Chuck's mother, his father's "beloved wife", died giving birth to him. When Chuck is bailed out of jail by his father's lawyer, he promises Dan he'll try to get him out, too. However, Chuck accidentally finds out that Dan was trying to get close just to use him for his writing. Enraged, he says to Dan he will regret messing with him and that he lied about his mother dying at his birth.
In episode 6, "New Haven Can Wait", while everyone is visiting college, Chuck and Nate stop at Yale University. He hopes to run into the "Skull and Bones" group, who eventually kidnaps him. He wants to become a member, and in order to do so, he must show his "worth" in several ways, including giving up Nate (who is hated because of his embezzling father). Instead of betraying his best friend, Chuck sends them to Dan, telling them he's Nate. The Skull and Bone's kidnap Dan, take off his clothes (except for underwear) and tie him to a statue. When Nate hears what he's done, Nate ends their friendship and befriends Dan, leaving Chuck alone. However, Chuck does triumph against the Skull and Bones by revealing he had faked wanting to be a member in order to gain incriminating pictures of them. Thus, he “owns” the future leaders of America.
In Episode 7, "Chuck in Real Life", focus is shifted once again to Chuck’s pursuit of Blair. After telling her they are “inevitable” she asks him to “seduce and destroy” Vanessa Abrams (who attempted to blackmail her) in exchange for an intimate night with her. Chuck is told to pretend to buy an old Brooklyn speakeasy, but when he visits the place, he truly likes it and finds a newfound respect for its owner and Vanessa. She, too, realizes there is more to him than his playboy façade, especially after she witnesses Chuck being unfairly berated by his father, Bart. Blair, jealous at the sight of them holding hands, reveals to Vanessa their original plot thus humiliating her, causing Chuck to “win their bet.” Chuck later tries to smooth things over at the speakeasy, but has lost their trust. He then returns to Blair and the two of them begin to passionately embrace until he pulls back and asks her to say the “8 letters, 3 words” she wanted him to say before. When she responds that she will never say those words to him, he tells her that she will “never have him” then and that he's chased her for long enough, and it is now her turn to do the pursuing. He then walks out, leaving a stunned and upset Blair behind him.
Chuck begins pestering Blair to say "those three words." Blair is adamant about not saying them because she believes that saying them would mean Chuck would win. Her plan is to completely ignore Chuck, however Dan suggests that instead she become unavoidable, which would end up driving Chuck crazy. Blair nearly seduces him in Serena's bedroom, but Blair's cell phone rings right at that moment with a text message from Serena herself. She tells him to ignore it but he becomes suspicious and they simultaneously jump on the bed to grab the phone. Chuck wins and reads the text. Chuck realizes from the text that Blair has nearly tricked him out of his demand, and angrily leaves the room.
Blair eventually decides that she is going to drop the fight and tell Chuck she loves him. At the last minute, however, Dan (fueled by his anger for what Chuck and Blair did to Vanessa) tells Blair it is probably a mistake and that she should be sure that Chuck isn't playing any more games. Blair meets Chuck on the roof of Rufus' art gallery, where she unwillingly begins to break down and cry, telling Chuck how humiliated and hurt she felt when he never showed up at the airport, forcing her to make the trip to Tuscany alone. Chuck dismisses this as old history and expresses his disappointment that Blair still can't tell him she loves him. She leaves in tears, and Serena, seeing this, confronts Dan about the faulty advice he gave her. Dan realizes then that he is sorry he sabotaged Blair and finds Chuck to tell him that Blair was going to tell him the three words before he stopped her. Later that night, Chuck goes to Blair's room and tells her that he thinks the reason why neither one of them can say that they love each other is not because it isn't true, but because that would mean giving up the "game" and falling into the more traditional boyfriend/girlfriend role, which both admit would be the death of their passionate relationship. Chuck tells Blair that he believes they should wait for better things in the future, and she agrees, saying that "there could be some excruciating pleasure in that".
In episode 9, "There Might Be Blood", Blair babysits the teenage daughter, Emma, of a prominent Yale alumni. Emma is intent on losing her virginity before her best friend does and attempts to enlist Chuck to do so. However, Chuck is unable to do it, prompting Emma to run off to a club to find a man who will. Chuck tells an angry Blair that the backseat of his limo is a sacred place, alluding to Blair losing her own virginity there in Season 1. Blair drags along Chuck and Serena to track down Emma, and Chuck uses his pull to have Gossip Girl post a fake article about Emma's best friend losing her virginity. When Blair thanks him, he says, "For you, anytime." Later, when Blair is bringing a disappointed Emma back home, she tells her that a girl's virginity is special and that she should lose it to someone she really loves. When Emma asks if Blair lost it to someone she loved, Blair says yes.
Chuck and Blair decide to pick each other's dates for the annual Snowflake Ball, since they know each other the best. If Chuck actually likes his date, Blair gets his limo for a month; if Blair likes hers, Chuck gets Dorota, Blair's maid. Both end up picking slightly less glamorous look-a-likes of themselves. They find them hooking up by the end of the night, which upsets Blair, who wonders why even "Beta Chuck" and "New Blair" can work it out when they can't. At the end of the night, Blair and Chuck end up resolving their differences and enjoy the night dancing, but the happy peace is interrupted when Lily, Chuck's stepmother, comes with some bad news. Bart Bass, Chuck's father, has died in a car accident.
Mourning his father, Chuck reverts back to his old alcoholic ways, spurning his step-family and his friends, and attempting to buy out the secret about Lily that Bart's PI had uncovered shortly before Bart's death. He largely blames Lily for Bart's death, having seen her with Rufus at the Snowflake Ball. Lily, who fears that Chuck may discover her secret, counters that Chuck is the reason Bart is dead, since he had called Bart telling him to come check on his wife, which led to the fateful limo ride. Chuck arrives at Bart's burial completely drunk, supported by Nate and Blair, where he lashes out at Lily, the other van der Woodsens, and the Humphreys. He tries to leave afterwards, to which Blair tries to stop him by finally telling him that she loves him. Now a broken man, Chuck does not respond in a kind way. Instead, he coldly tells her,"Well that's too bad", confirming his earlier statement, "You're not my girlfriend." Chuck purchases the information from Bart's PI after Lily's mother, Cece, withdraws her bid without Lily's knowledge, but Lily persuades Chuck to learn from his father's mistakes and let the people who love him in. As a part of this change of heart, Chuck burns the information and crashes Blair's mother's wedding, where Blair takes pity on him, comforting him tenderly as he sleeps beside her. However, Blair awakes in the middle of the night to find that Chuck has left, leaving only a note in his place, which says, "I'm sorry for everything. You deserve much better. Don't come looking for me." The episode ends with Chuck's whereabouts unknown and Blair sitting on her bed in tears.
During the episode "In the Realm of the Basses", Chuck returns after his uncle, Jack Bass, finds him in Thailand. He cruelly shuns a hurt Blair, who is still waiting for him to tell her he loves her. He is caught smoking hash at school, and is suspended, despite Blair's pleas on his behalf. He buys back Victrola, now that he is about to inherit his father's large fortune and throws a party. During the festivities, he drunkenly goes up to the roof, on the brink of suicide. Blair and Jack follow to find him shouting, "I'm Chuck Bass! No one cares." Blair fervently declares, "I do!". With tears in her eyes, she reminds him that everything he is doing to himself hurts her too. After telling Chuck "I'll always be here," they embrace, and Chuck apologizes.
At the reading of Bart Bass's will, Chuck and Jack are stunned to find that Bart has bequeathed to Chuck the majority stake in Bass Industries. Jack, who wants Bass Industries for himself, is furious that Bart chose his teenage son over him.
Jack comes up with a plan to set Chuck up for failure. When Chuck mentions that he is going to have dinner with Blair, Jack asks Chuck if he is the kind of guy that would "spend all day at the office then come home to a wife?" and also informs Chuck that his father's best success happened when Bart was single. He coaxes Chuck into ditching Blair for a night on the town, complete with alcohol, drugs, and strippers. Chuck can't resist, and cancels on Blair. Meanwhile, Jack convinces Blair to throw a celebratory brunch for Chuck for taking over Bass Industries. When Blair and two members of the Bass Industry board look for Chuck in his new office, as Jack had suggested, they find Chuck, obviously drunk, with two lingerie-clad prostitutes and a desk littered with drugs. The board members express their disgust, and a confused Chuck lashes out at Blair, saying, "I don't need your help. Stop trying to play the wife!"
Chuck later confronts Jack about this, clearly hurt that his uncle would set him up. Jack points out a loophole in Chuck's acquisition of the company, the morality clause, which dictates that the board members can replace Chuck with his legal guardian, Jack, if they find him unfit for the job. Jack gloats that he has talked to the board members, all of whom were more than happy to hand the reins over to Jack, and he now has control of the company.
Realizing all he has left is Blair, Chuck brings her a bouquet of flowers and apologizes for all that he did. Blair says that she can not be there for him anymore and she then throws his bouquet of flowers in the elevator with Chuck as the doors are closing the next morning. Having lost his father, his company, and the one person left who still loves him, Chuck is seen throwing his tie at a picture of his deceased father, having failed him due to his own insecurities.
In "You've Got Yale", Chuck pairs up with Lily van der Woodsen to bring down his uncle (Jack). After a few failed attempts, including getting Jack on a list of sex offenders and ordering Anthrax from the black market on his credit card, Chuck seeks his ex stepmother's help. Later, at the opera, Lily remembers that whoever is Chucks legal guardian own the majority of the company. She then asks Chuck if he would be willing to let her adopt him as a son, as was his dead father's intention, and Chuck gladly accepts, therefore Lily becoming Chuck's adopted mother and legal guardian. Infuriated at losing the company, Jack confronts Lily in the powder room, attempting to rape her, but is luckily apprehended by Chuck in time. Chuck punches his uncle, and Lily thanks him. The next day Chuck asks if he could still move in with his now legal adoptive mother to which she joyfully agrees. Lily also tells him that as soon as he turns 18, Chuck will inherit his fathers company—saying that "[she] doesn't want the company, [she] just wants [Chuck]".
In "The Grandfather," after Blair gets rejected from Yale, she goes on a rampage similar to Chuck when his father died. Chuck and Serena follow her to Nate's family reunion where she's insulted all the elite guests. Chuck pulls her aside and tells her that this isn't her real self, saying that he "knows her better than he knowns himself." Blair, in return to that comment, pushes Chuck up against a wall and attempts to seduce him, telling him to "take her now." Chuck, however, refuses saying that this isn't the Blair he wants. Blair becomes furious, saying that "She never will be again" and walks away. Now depressed, Chuck is drinking in a room all along where Serena finds him. He confesses that he is losing her, and Serena tells him to fight for Blair, like she did for him.
Chuck continues to pine over Blair, and grows jealous when he sees Blair and Nate becoming close, and developing a friendship. He accuses Blair of being in a relationship with Nate, but when she denies this, he still does not believe her and tells her that her relationship with Nate had no "spark". Where Blaire replies "we have many sparks, even fireworks." Chuck then says to her "That was us" So Chuck conspires with Vanessa, who has broken up with Nate, to come between Nate and Blair, however, when Vanessa sees Blair and Nate together at a party, she kisses Chuck and the two have sex. They later agree to keep this a secret, but Blair and Nate enter into a relationship of their own, regardless.
In "The Wrath of Con," Chuck admits he loves Blair but can't be with her because he can't make her happy, so he lets her go.