The season opens up with the school janitor Desmond finding a positive pregnancy test in the girls bathroom. When Trisha get's a hold of it, she goes and confronts Brittnay, thinking it's hers, but Brittnay denies it, claiming she's saving her "vaginity" for someone special; then they find Mackenzie to see if it's hers, finding out it isn't, and it's not Trisha because her boyfriend was born without genitals. Quickly they realize it could be Shay's test, and they go find her to gloat about the fact she'll get fat, but Shay denies it's hers also. The test actually belongs to Saison Margeurite and Blaine, causing Brittnay to go into hysterics and even thanks God for the news.
Meanwhile, Rachel Tice and Judith go to school after winning prom, believing now they'll be apart of the popular girls; they go up to the cheer squad in hopes to hang out and do "popular girl stuff" but the squad shuns them, and verbally insults them. As they walk away, Ashley Katchadorian appears mysteriously and asks if they want revenge on the cheer squad, but they turn it down. In the next episode, the football team tries to coach Blaine on being a father, trying to give him a football to nurture as his child, but keeps throwing it. Than appears and makes his usual homosexual insults at the team (while sounding like he'd like to act on the insults as well), but he states that he's straight and has sex with a lot of girls, "like 12 or 2". He bets them he could go have sex with any girl he wants, so he goes and talks to Brittnay, instigating that they should. At first she's repulsed by him, but later turns out to be attracted to his "mixed messages" and she allows him to have sex with her, but to her it's so she can get back at Blaine (they dated briefly in the second episode of the first season, but broke up when Brittnay found out he liked Gossip Girl more than Glee).
Then, after a visit to the doctor, Mackenzie finds out she has FPD (Female Pattern Baldness), and planned to tell Trisha and Brittnay, but suddenly they're confronted by the Atchison cheer squad, Tanya Berkowitz, Taylor McDevitt, and Trisha 2, who aren't allowed at the Overland Park mall due to chear squad law. They come to their mall because their mall burned down. A feud is quickly escalated (even though both Trisha's become friendly with each other), and they decide to settle their dispute at cheer nationals to see who can actually "own" the mall. Meanwhile, back at school, Saison is the subject of a reality show, "Babes Having Babies", which the filmmakers refer to it as "kind of like 16 and Pregnant, but we film them for the first two months of the pregnancy, you know, before they get all fat and shit". Saison says Brittnay is her best friend, and Brittnay plays along soley to get an opportunity to be on TV.
For nationals, the cheer squad tries practicing, but the team faces problems: they only have five members seeing as how Jenna Derabon has been missing for some time, and, unknown to the rest of the squad, Ashley Katchadorian is siding with the Atchison squad in an act of revenge for what Trisha did to her. They hold tryouts, and the only person qualified is Saison, whom one of the producers of Babes Having Babies forces into the squad after giving Brittnay her own show after a clip of her swearing and ranting about Saison becomes viral on YouTube. Then cheer nationals begin, and all of the cheerleaders are present except for Ashley. When she arrives, it's finally revealed that her evil plan was to switch sides for the Atchison squad, and leave the Overland Park cheer squad short a member so they wouldn't be able to compete, and also she taught the Atchison squad their routine. But before the defeated Mackenzie leads her squad away to go back home, suddenly Deandra appears wearing the Overland Park uniform, saving the cheer squad. When it's their turn to compete, they do their routine as it was planned, but in the end Deandra had the entire squad balance on her robotic arm, and it won them the trophy. An angered Tanya and Taylor scorn the squad but even with Brittnay's reality show filming and Mackenzie's FPB, they curse out the squad and they leave in defeat. But just when everything seems to be in the clear, a girl from far away watches them, cursing Mackenzie's name. It's revealed when Justin Michealson appears that the girl is actually Jenna Derabon, a former member of the cheer squad, and she's working on her revenge against Mackenzie.
The creators and producer of MPGiS announced on Feb 7, 2013 that they will be accepting donations for Season 2 sets, constumes, and characters at kickstarter.com. In exchange for a donation, the creators of the show will send donators things like autographed scripts or your name featured in the show. However, the kickstarter project has ended and the producers well exceeded their goal.