The glee club win the Sectionals round of competition, advancing on to Regionals. Finn discovers he is not the father of Quinn’s baby. Ken breaks up with Emma over her feelings for Will, who leaves Terri and shares a kiss with Emma.
When the glee club are left out of the school yearbook, Rachel has the team cast in a local mattress commercial in an attempt to raise their social status, but her actions inadvertently result in them becoming ineligible to compete at Sectionals. Will discovers that Terri has been lying to him about being pregnant. He steps down as club director so that the team is eligible to compete, but remains undecided over whether to end his marriage.
Sue gives New Directions’ set-list for Sectionals to the competing clubs in order to damage the glee club’s chance of progressing to Nationals. Quinn reconsiders having her baby adopted, but ultimately recommits to the idea, and Kurt gives Rachel a bad makeover, sabotaging her attempts to attract Finn.
The glee club members are split into pairs to sing ballads to one another. Rachel is paired with Will and develops a crush on him. Finn and Quinn’s parents (guest stars Gregg Henry and Charlotte Ross) learn that Quinn is pregnant, and she moves in with Finn and his mother when her own parents throw her out. Puck reveals to Mercedes that he is the father of Quinn’s baby.
The glee club hold a bake sale to raise money for a handicap accessible bus, so that disabled club member Artie can travel with them to Sectionals. Quinn struggles with the medical expenses incurred by her pregnancy, and Puck offers to support her. Sue accepts a student with Down syndrome onto the cheerleading squad, leading Will to question her motives, and Kurt and Rachel compete for a solo performance.
Will attempts to create a mash-up wedding song for Emma and Ken. Ken becomes increasingly jealous of Emma’s feelings for Will, and tries to force the football-playing New Directions members to quit the glee club. Finn and Quinn find that they are no longer considered popular. Rachel and Puck briefly date, but break up as they both have feelings for other people. Sue has a short romance with local news anchor Rod Remington.
Will and Sue clash over the running of the glee club. Sue tries to tear the club apart by turning the students against each other, but they rally to support Quinn when news of her pregnancy leaks throughout the school. Terri blackmails her obstetrician into faking a sonogram, deceiving Will into believing she is still pregnant.
Will pits the girls against the boys for a mash-up competition. Terri takes a job as the school nurse to stop him becoming closer to Emma, but is fired after giving the glee club performance enhancing pseudoephedrine tablets. Sue is appointed co-director of the glee club, and Emma becomes engaged to football coach Ken Tanaka.
Will recruits former glee club star April Rhodes (Kristin Chenoweth), hoping to improve the club’s chances in the wake of Rachel’s defection to the school musical. Finn flirts with Rachel in an attempt to convince her to return, and although Rachel is angry when she discovers Quinn is pregnant, she ultimately rejoins the club.
Will form an all-male a cappella group, the Acafellas, neglecting the club in favor of dedicating his time to the new endeavor. New Directions struggle with choreography, and resist attempts at sabotage by members of the cheer squad. Mercedes harbors romantic feelings for Kurt, who comes out as homosexual.
