The season takes place right at the beginning of the school year, after the events of Cheer Nationals in the summer. Mackenzie Zales and Brittnay Matthews are shocked to learn that Ashley Katchadorian was brave enough to show her face back at Overland Park High School after she betrayed them for the Atchison Cheer Squad at Cheer Nationals. Ashley explains that the commute was too long, so she had to come back to Overland Park and is planning to lay low. Jenna Darabond makes a triumphant return to the classroom, where the Cheer Squad once again is upset that Jenna decided to disappear through all their past year's drama. Jenna reveals she's been behind the scenes and the reason all the drama started with Deandra, Trisha, and Mackenzie in the bathroom. Jenna explains her reason for letting Deandra into the bathroom was because Mackenzie made out with Justin Michaelson, Ashley's boyfriend, even though she knew Jenna liked him. She let Deandra into the bathroom, calling herself Ashley Katchadorian, which is the reason behind the whole Trisha/Ashley conflict. Jenna then gets mad at Brittnay for making out with Justin at prom and decides to just get revenge on the Cheer Squad as a whole. She admits to setting the Atchison Mall on fire, causing the Cheer Squad to invade the Oak Park Mall. After the whole truth comes out, Mackenzie and Brittnay are furious, but Jenna explains tht her revenge has only begun. She plans to ruin their popularity with hipsterism, where everything that is cool will no longer be and everything that nobody wants, everyone will want.
Mackenzie first experiences hipsterism when she accompanies her sister, Katelynn Zales, at the Little Miss Overland Park Tots Pagaent. She discovers that Mikayla Van Buren is competiting in the regular pageant, but loses to a girl named Gwen Kindle, who no one liked. Mackenzie realizes that Jenna's plan of hipsterism is now coming into action after Gwen wins the pageant. The rest of the month seems to be pretty quiet, as Thanksgiving passes (with Deandra's celebration of Thanks! Give Me!). In the beginning of December, the cheerleaders are shocked to learn that since Jenna Dapananian left, the squad is down to three people. After finding out that their pep rally for winning Cheer Nationals is cancelled and replaced with a farmer's market, the squad is horrified to see hipsterism in action again, meaning Jenna is determined to take down the cheer squad once and for all.
With the squad being down to three people, they see the perfect opportunity to get new members by putting up a booth at the club fair. Jenna creates the Overland Park High School Student Collective alongside Jenna Dapananian, and promotes the club to Judith, Rachel, and Than, who gladly accept their offer to join. Later, the Cheer Squad is horrified to learn that Justin Michaelson is now a hipster too, meaning that if Jenna can change one football player, she can change all of them, and eventually the entire school. Justin also quits the Football Team as a result of joining the hipster movement, though they remain friends. The holidays don't seem to work out as well (Trisha and Mikayla's friendship is discovered by Mackenzie and Lunch Lady Belinda creeps the Mall Santa out). To make matters worse for the cheer squad, nobody else other than Deandra attended their New Year's Party and reminisce of what happened back then.
The cheer squad finally decided to get their new members because only 3 people is not enough to destroy the hipster movement. Brittnay convinced Saison to join the cheer squad for the second time, however they are still not in good terms. Mackenzie reluctantly brought Shay into the cheer squad, but only if she can be the head cheerleader. Trisha brought in Trisha 2 (however, she was supposed to get Ashley Katchadorian). Shay brought Dr. Greg Converse to help the cheer squad become the better, more popular and sassy cheer squad they were to be. In addition, they modified the uniforms (because Dr. Converse disliked how the concept of the old uniform has no connection to the school). The Football Team also got new recruits to replace Justin (Than and Deandra). Unbeknowst to them, Than was with the hipsters.
Mackenzie had a horrible nightmare that Saison gave birth to a hipster baby and clashes with the vain and arrogant Shay. Than was still unsure whether to be with Jenna and the hipsters or the popular, athletic crowd. Meanwhile, the cheer squad (and Blaine) see the hipsters wearing the old cheer uniforms (claimed to be vintage). Mackenzie rants to the hipsters that she's the Queen of Revenge and she'll not stop until they are done for. The cheer squad meet up at Shay's house to make a plan to jack the hipsters up. Brittnay suggested punching Jenna in the face, but Shay declines it, saying that if she (Brittnay) did that, Jenna will just report it to the school and they'll have 4-hour parent-teacher conferences. The cheer squad was unable to give out great ideas for their plan to harass the hipsters, such as Brittnay's idea to light their cars on fire and/or punching Jenna in the face, the Trishas' poor contribution and Shay not thinking of something very original.
Mackenzie was able to think of a great plan; the first phase is to follow the hipsters around their favorite places and getting there before they do, such as Scooter's Coffee (the hipsters' coffeehouse), the thrift store and even the abandoned alley. The football team watch their opponents on TV and their strongest player, 22 year old Oisin McGrann, aka The Bone Breaker. Later, Mackenzie, Shay and Brittnay were shocked to see the latter's car burning to ashes, but, disregarding Shay's parent-teacher conference warning, Brittnay punched the curious Jenna in the face (thinking she burned the car in retaliation for the follower prank moments ago but later was Mackenzie who did it as part of the plan she came up with before) and puts the cheer squad (except Saison and Trisha 2) in a dangerous situation.
Mr. McNeely supervises the parent-teacher conference and tries to make the parents think of a way to resolve the problem after a huge arguement with their daughters due to the events of what happened the previous day, but, thanks to their poor parenting skills, he came up with a way; if he hears of an incident from the cheer squad again, he will revoke cheerleading for the rest of the year, including State Championship. Brittnay disregards Mr. McNeely's punishment and destroys what was probably Jenna's locker with a metal baseball bat. Unfortunately for her, it was not her locker. Jenna also gives Mackenzie and Trisha invites to their hipster concert, named "Hipchellastockalooza". The concert was scheduled on the same night as the state championship, and was staged on the parking lot of the stadium, meaning whoever wants to watch the football game has nowhere to park. Meanwhile, Saison gives birth to her baby in the canteen with the help of Deandra, Trisha 2 and Lunch Lady Belinda.
It was time for the state championships and 3 leaders (Mackenzie, Jenna and Matthew) gives out pep speeches to their respective groups to motivate them and claim the night as theirs. Brittnay and Trisha 2 are considered for the godmother role for Saison's baby, but Trisha 2 quit, resulting in a reluctant Brittnay being the godmother. The first half of the game ended in a tie (14-14), and Deandra gives the football team a pep speech that would help them defeat the opposing team and Oisin McGrann. Meanwhile, Than was having trouble choosing between the football team or the hipsters (Jenna wants him to make the team lose state, while the football team starts to like him), and was convinced by Damian Lewis (who was there because one of his friends is a drummer for a Hipchellastockalooza band) to follow his heart, though he still refers to him as Brody from Homeland.
Justin breaks up with Jenna because he saw her and Than locking lips, and quits the hipsters as a result. The hipster crowd (notably a Cher fanatic, Ashley, Connor Devarnan and Amberlynn) were getting bored with the concert, and they were convinced they'll just like what they like instead of following the latest trend and ditch the concert for the football game. Tanner was seriously injured during the game, and Than was trying to drop the subject. Mackenzie brings out cops to help the cheer squad bring the hipster movement to an end.
The concert no longer has an audience, so Jenna decides to go to the stadium to tell Mackenzie off and bring the crowd back. Mackenzie brings out the cops to arrest her for burning down the Atchison Mall, and uses Deandra's voice recorder as proof. Jenna demands that her father will help her get out of it, but it was no use anymore because he resigned from office ever since he began dating Cameron Van Buren, leaving his family and being involved in a sex scandal. Mackenzie reveals that she called Senator Darabond to the parent teacher conference, as well as Cameron.
While thinking of a plan to obliterate the hipster movement, Mackenzie thought of an idea; distract Brittnay with the follow-the-hipsters plan, then have her car burned so she can punch Jenna in the face thinking she did it, establishing the parent-teacher conference that brings the senator and Cameron together which will help Mackenzie arrest Jenna easily. It wasn't Jenna who blew up Brittnay's car, but it was none other than Mackenzie, shocking everyone, especially Brittnay who said that Mackenzie used her, but she had to take care of what had to be done.
Meanwhile, Than was persuaded in his mind (Jenna wants him to throw the game but the football team started liking him), and ultimately chose the football team as knocks Oisin McGrann out. Tanner wasn't able to finish the game now that his arm is broken, and Blaine has to play quarterback but he is unsure who will be tight end. Justin rejoins the football team and as a result, they won the entire game.
Mackenzie declares that the cheerleaders have regained popularity as they and the football team take a group picture while Brittnay ignores in fury. Moments later, she crosses out Mackenzie's face in the picture and tells it that she is done. Meanwhile, Jenna receives a visitor in prison, who turns out to be Tanya Berkowitz. In revenge for blowing up the Atchison Mall, she brutally injures Jenna through stabbing and leaves her to pass out, concluding the season.
Like for season two, the creators are asking viewers and fans to donate to help fund the new season, and those who donate will receive exclusive T-shirts, stickers, notebooks, a DVD of the show's first two seasons, and more. The kickstarter ended, and the creators made their 20K goal before the last day.