Despite not having Saturday detention, Grover Jones attends anyway just to be near the girl of his dreams, Violet Adams. When a nearby chemical plant explodes, they find themselves trapped in the school along with his sister Mary, basketball players LaShawn and Noodle, Lashawn's girlfriend Zoe, bully Diesel, computer whiz geek Barrett, and Natalie while the other students venture outside to try and find any survivors.
As Grover, Violet, Barrett, and the Coach try to get more answers from Lyle, more students show up, all experiencing the same symptoms. They go to sleep momentarily, and wake up as zombies. The remaining check on food and supplies. As Grover and Mary try to bring food to a sleeping Coach, only to find him being eaten by the reanimated "freaks". Grover and Mary barely manage to escape and barricade the freaks inside. Mary goes to the bathroom to try and catch her breath, and is revealed to have been bitten.
Grover learns that Mary has been bitten, and starts bringing her supplies. However, Mary slowly starts experiencing the symptoms and begins acting strangely toward other people. Barrett tries to establish contact on a CB radio, but does not initially get help. However, when no one is looking he plugs in the radio and speaks with an unknown person. He is caught by Mary, who tries to tell the group. The freak instinct comes over her and she prepares to eat him, but Grover intervenes. The remaining survivors become suspicious of Grover, and Violet is the one who defends him when the truth comes out. Mary goes to sleep, but a few hours later wakes up a freak.
Grover goes in to check up on Mary, but is shocked to learn she has become a freak. Mary escapes, and the group splits up to look for her. LaShawn and Zoey manage to find her in the locker room (and also a dead Noodle). Zoey barely escapes, and Mary is knocked unconscious. She is locked up as the remaining group decide what to do. Grover manages to convince them to keep her alive. Barrett goes down later and burns her with a flame in order to learn more about the freaks. Grover finds out and gets mad, but the group takes a vote to either keep her alive or continue testing on her. The votes are tied, with the deciding vote being from Violet; they agree to keep testing. Grover angrily goes to confront Mary, and the episode ends with an implication that he is going to kill her.
It is revealed in the opening minutes that Grover did not go through with killing Mary, and along with Diesel helped her escape to the outside. Lashawn is acting strangely, and the kids begin to suspect he might be infected, but it turns out that he is running low on insulin. Grover and Barrett find two more vials, and Barrett puts one in his jacket while giving the other one to Zoe, but at a cost. Zoe and Barrett strike an uneasy alliance. Grover is still angry with Violet, but later make amends and dedicates a wall in memory of their fallen friends and teachers. Diesel arrives with more bad news, that the plumbing stopped working and that the water is gone.
While the group carefully rations everyone's remaining liquids, Grover discovers that the fallout shelter stores gas masks that will enable them to escape. Violet plans to make knockout gas for use on the freaks so they can go in and retrieve the masks. She and Zoe climb through air vents into the chemistry lab to gather the necessary chemicals, and while at it battle a freak. After the successful mission, LaShawn and Zoe intimately make out, and she and Natalie make amend their relationship, reuniting as friends. Grover and Violet grow closer and dance together while Natalie reveals to the rest of group of her pregnancy with the help of Zoe's advice. Unbeknownst to them, the freak that Violet was believed to have killed survived and manages to enter the air vents.
Grover walks in on Barrett secretively talking to people on the radio and rats him out. Violet, losing her temper, knocks him out with the newly made sleeping gas, unintentionally getting Diesel too. This mistake prompts her to privately record herself revealing how she believes she caused the chemical plant explosion and the disaster following it. LaShawn, Grover, and Violet take on the mission to go in the shelter. Barrett wakes up, and Natalie tries to warn Violet. They find out Grover got knocked out by the gas, but are too late and are forced to leave him trapped with the now awakened freaks. Eventually they find a way to run in and save him, and succeed, while Diesel, Barrett, and Zoe fight the freak that escaped through the air vents. The group celebrates as the others come back with all 7 gas masks and commend Grover, but things take a bad turn when they discover that only one of the masks work.
The group decides to draw a name from a bowl to see who has to go outside for help after the water gets shut off. Diesel is originally chosen but because of his claustrophobia he isn't able to wear the mask without hyperventilating, so they chose again. Barrett pulls Zoe's name, but lies and says that it's LaShawn's so they prepare him to go outside. Diesel feels guilty about not being able to go, but Natalie comforts him telling him it wasn't his fault. Eventually they loose contact with LaShawn and they fear that he got hurt. In the end a stranger shows up at the door and says that he is with Rescue and Recovery.
John Collins introduces himself and tells them that he'll be taking them somewhere safe. Despite having a hazmat suit he claims that he has a vaccine for the air outside and tells them to pack their stuff so they can get going. Barrett is suspicious of the vaccine and decides to steal one and test it on Mr. Oink. Grover believes that Barrett is just causing problems until he sees the effect the vaccine has on Mr. Oink. Collins knocks out Barrett and Grover when he sees that they've figured him out, and they are too late to stop him from injecting Natalie with the poison.
In the season finale, things come to a head when John Collins is revealed to be a traitor and Natalie to be dying from the poison. The group becomes aware of shocking secrets behind the chemical plant. The group attempts to hold Collins hostage but he manages to escape, Diesel is shot in the process but survives. Violet is captured and Collins demands his suit in return for her life. Grover and the group comply to his demands, but secretly attach an alarm to the suit. But Collins secretly removes the basement shelter door barricade as well. The alarm on his suit goes off after exiting to the outside, attracting freaks that kill him. Diesel and Natalie share one last moment with each other before she sacrifices herself in order to save the others when they are about to lose against the freaks that have suddenly escaped the shelter. Diesel and the other remaining four survive are left in grief. Afterwards, it is shown that Grover had uncovered a photo of himself from Collins' bag which labeled him as a retrieval target. In the final scene, Lashawn, whom they all thought was dead, turns out has survived and returns, informing Zoe and Barrett that he had no choice but to lead new survivors to the school.
