After a tough loss at Regionals, the glee club is back as the underdogs of McKinley High. When the school is faced with even more budget cuts, Mr. Schuester pushes the kids to help recruit new members for the club. Rachel and Finn disagree on new recruits, and aren't sure they will be able to come together in perfect harmony.
When Brittany and the gang try to convince Mr. Schuester to let them do a Britney Spears number, he is reluctant to go that edgy. Meanwhile, an insecure Will is curious about Emma's new beau, Dr. Carl Howell, so he convinces her to bring him in to talk to the kids about dental hygiene. While the dreamy doc inspires the girls to take their dental health more seriously, Will is left feeling worse than before.
Finn has an existential crisis when he believes he sees the face of Jesus in his grilled cheese sandwich. Meanwhile, the rest of the kids rally around Kurt after he has a crisis of his own that leads to a larger discussion among the group about their own theology.
After Finn and Sam find an unconventional way of controlling their urges, a few glee club members pick up on the strategy and start using it too. But when Coach Beiste gets wind of what they are up to, the glee club has some explaining to do.
When Mr. Schuester gets sick, a substitute teacher takes over his Spanish class and the glee club, and winds up winning over the whole New Directions clan. Meanwhile, when Sue fills in for Principal Figgins as McKinley's top dog, she tries to flex her power on campus.
To prepare for sectionals, Will wants the spotlight on the team, so, to Rachel's dismay, she has no solo. Meanwhile, Kurt is brimming with ideas that don't fit the eight-part, no-standout harmonies of his new school. Behind the scenes, Puck must find a replacement for Kurt or they're one-short of eligibility, Will is losing Emma, Tina and Artie suspect Mike and Brittany of surreptitious romance, and Santana spikes Rachel and Finn's relationship with a revelation. Can the club overcome divisions and jealousies to win sectionals?
Finn tries to bring a little holiday cheer to McKinley High, and Artie discovers that Brittany still believes in Santa. Meanwhile, the teachers pick their Secret Santas, and one manipulative coach rigs the gift-giving in her favor.
Mr. Schuester and Coach Beiste devise a plot to bring together the warring glee club and football team factions. Meanwhile, Sue, desperate to win cheerleading Nationals, launches a dangerous plan to bring home a trophy, and the New Directions tackle Michael Jackson's iconic hit "Thriller."
The boys find the Valentine's dating buzz dying down makes scoring hard. Sam finds a way out that works so well even Fin ends up begging permission to join what seems so childish: a Justin Bieber tribute. Sue seems suicidal after loosing her cheerleaders budget, so Will naively lets her observe and possibly join the glee club, despite the kids' protest. Once in, she decides to spy and successfully postulates for coach of a nemesis rival team after 'freeing' that post. Rachel pays Brittanny to become a fashion idol, only to find she created a monster.
Principal Figgins expects the glee club to help promote Alcohol Awareness week. Schuester eagerly accepts and chooses it as song selection theme, but Sue maximizes Will's embarrassment after discovering he let coach Beiste drag him along to a country bar with song, dance and alcohol. The kids can't resist the forbidden fruit that is dangling before them, only to be cured by their hangovers.
Schuester volunteers to program Glee club songs which help with sex education, hearing many of his kids are dangerously ignorant. Free-spirited substitute sex-education teacher Holly Holliday therefore comes help him select and arrange appropriate repertoire. That proves tricky, as does the kids' own input, also on account of their personal (romantic) agendas. The Celibacy Club welcomes unlikely recruits.
Saddened by the death of the Warblers' mascot bird, Kurt speaks out against Blaine singing every single solo. To his surprise, Blaine agrees and insists they perform duets, privately adding that's also an excuse to spend time together. Blaine also convinces Kurt's father it's time to contribute to his sexual education. Sue successfully spreads a rumor so as to trick Will into opting for originally composed songs, a very tall order, while her choir caters to the jury members' bizarre tastes. Fin coaches Rachel to write from real life emotions.
Proving that birds of a feather flock together, when another under-the-radar club at McKinley High needs helps raising funds, the glee club signs up to help. But when Sue hears about the show of support, she moves quickly to put the kibosh on it. Meanwhile, relationships are tested and big decisions will be made.
Mr. Schuester teaches the glee club a valuable lesson about self-acceptance and embracing what makes you unique. Meanwhile, Lauren and Quinn go toe-to-toe for the prom queen crown, Ms. Pillsbury confronts her obsessive issues, Rachel struggles with a life-altering decision and Santana has something up her sleeve that could permanently alter the glee club dynamic.
Sue Sylvester revives the school newspaper and decides to print a few inflammatory blind items. The glee club gains a whole new respect for Sam when they discover some interesting new information about his family life. Meanwhile, April Rhodes returns to Lima and tries to convince Mr. Schuester to hit the road with her.
Multiple former winer Jesse St. James has been hired as consultant to prepare for the nationals. He gets Will to organize soloist auditions, at which he tries to undermine everybody's confidence before applauding Rachel. Meanwhile Fin and Kurt, who each lost a parent, volunteer to help boxing and insist the choir must perform at the funeral of arch-enemy Sue's beloved, utterly different sister Jean Sylvester.
After undoing Sue's travel sabotage, the Glee Club arrives in New York. They still have to write original songs, but use inspiration as excuse to wander around first. Broadway is Kurt and Rachel's dream, so they wonder trough Manhattan. Will is found out tasting a solo part, but decides to stick to teaching. Although Fin dropped his girl-friend for her, Rachel decides to give her 'career' priority. That leads to him kissing her on stage, possibly the reason they don't make the final ten.