Ben is not a character in the novel series, so the two do not have any form of relationship.
Nate meets and eventually begins dating Juliet Sharp, who has an obsession with destroying Serena (Belles de Jour). Serena meets Colin Forrester, cousin of Ben and Juliet, and the two begin to flirt despite him being her professor (Easy J). When Juliet finds out, she encourages Colin to stay away from her, but Colin is more angry at her still being in contact with Ben (War at the Roses).
In Juliet Doesn't Live Here Anymore, Colin quits teaching at Columbia to be with Serena, but the two break up anyway. Soon after, Page Six posts an article about Serena sleeping with a professor. While Serena and Lily save her from being expelled, Lily admits to Rufus that this isn't the first time Serena has ben accused of having an inappropriate relationship with a teacher.
In The Witches of Bushwick, Juliet, Vanessa Abrams, and Jenny Humphrey band together to take down Serena. At Chuck Bass' masquerade ball, Juliet and Jenny toy with Dan and Nate's emotions by pretending to be Serena and they kiss them. After the ball, Juliet drugs Serena and leaves her in a hotel room in Queens before going out and doing drugs dressed as her. When Serena finally wakes, days later, she manages to call 911 and is taken to the hospital. At the hospital, Lily realizes she needs help and involuntarily commits her to The Ostroff Center. Jenny, upon finding out how seriously Juliet hurt Serena, tells Blair Waldorf what they did. Before leaving town, Juliet tells Ben what she did. However, Ben is not happy with what she did and tells her she went too far (Gaslit).
In The Townie, Serena enters therapy and she tells the story of her in Ben. When she left town after sleeping with Nate (before Pilot), she ended up in Cornwall, Connecticut and started boarding school. Ben was her English teacher, and being attracted to him, they began to spend time out of class together; either studying or other academic activities. Both begin to develop real feelings, but Ben is strict on not crossing the line. One night, they're traveling back from a different state after visiting a library but their car breaks down. They find an inn, and Serena attempts to get a room with Ben. He rejects her, and unbeknownst to the two of them, Damien Dalgaard witnesses the whole thing. They stop speaking after that. Soon after, Serena wants to return to Manhattan but Lily is unable to get her into an acceptable private school with her records. She pays a visit to The Knightley School, and overhears girls gossiping about Serena and Ben. Lily uses that information to get Serena a transfer, but the state then launched an investigation against Ben. He is fired, and the state presses charges against him for transporting a minor across state lines and statutory rape, thanks to an affidavit signed by Serena. He is pushed to take a plea deal by the DA to serve prison time but be able to be off the sex offender registry and no record.
After Juliet explains things to Serena, she denies signing any paper and realizes Lily must have. She confronts Lily at her holiday party, and Lily admits to doing it. Feeling guilty, Serena begins a hunt to track down Ben and get him out of prison.
In The Kids Are Not Alright, Serena returns to New York to tell that she can't access the affidavit because the case involved a minor, and is sealed. With the help of Chuck, she is able to find a copy in Lily's safe at the bank and she attempts to blackmail Lily with it. At the same time, Eric discovers that Lily was putting up the judge in a hotel when Serena went looking for him. Lily begs Serena not to blackmail her because if the information ever got out, they would all face catastrophic backlash. Meanwhile, old Bass enemy Russell Thorpe returns to town intending to destroy Bass Industries. That night, Serena tries to see Ben in prison but learns he was released. She catches him outside and they go out for coffee. In Damien Darko, Ben tells her about his plan to move to a friend's place and help him with outdoor activities. Serena is sad, and asks Rufus if Ben can move into the loft with Dan instead. In Panic Roommate, Serena invites Ben to the W Magazine Party in hopes of finally winning him over. He tells her that he has no feelings for her, and never has. Meanwhile, Dan, Eric, and Damien plot to get Ben out of town. Damien has Eric punch him and then lie that Ben did it, which gets Ben sent back to prison for violating his parole. After Eric discovers Damien as using him, he tells the truth and Ben gets released. The next day, Dan apologizes and Ben reconciles with Serena; revealing he does have feelings for her.
In It-Girl Happened One Night, Ben lies to Serena about his Valentine's Day plans; not wanting her to know he became a cater waiter for the night. Serena unknowingly attends the party he's working at, Chuck's fundraiser party. However, the issue isn't too big and they make up by the end of the night. At the same time, Damien blackmails Eric with the information that Lily forged Serena's signature. In While You Weren't Sleeping, Eric feigns being sick to help Damien carry out a drug deal. Serena finds out, and promises to help; despite Ben warning her not to get involved. Being 18, Eric writes Damien a check with the amount he owes and Damien almost escapes before being caught by Ben, and threatened. Vanessa witness Ben get physical with Damien. At the end of the night, Ben returns the check and is cautiously welcomed into the VDW's home. Needing money, Damien informs Russell about Lily's crimes.
Ben's mother comes to visit in Empire of the Son, and is upset at Ben dating Serena, since she sees her as the person who ruined his life. She steals the affidavit, and gives it to Russell. Serena blames Ben, but realizes she's wrong. Ben breaks up with her, due to their history getting in the way.