The episode starts off in the living room with brothers Malcolm, Dewey, and little Jamie watching television. While getting popcorn, Reese is disappointed that he missed seeing a big flash and some fire. We think they're watching an action movie until Lois enters and yells at Hal to stop fooling with the TV, just as he's shocked once again.
After the opening, we see Hal, Lois and Malcolm at the kitchen table. Malcolm tells us that he's been accepted to Harvard and they're desperately trying to figure out how to come up with the money through scholarships, financial aid, grants, etc. As it is, Malcolm will be working three shifts in the college cafeteria, two in the bookstore and will be mopping the dorms at night. With all this, they're still $5,000 short. Hal is determined to find the money somehow.
Reese boasts that it's too bad Malcolm's future isn't settled like his -- he's the new assistant janitor ("all mop and no paperwork") at their high school. Craig enters with some of Reese's stuff all packed up. He can't wait for Reese to move in and Lois can't wait for him to move out, much to Reese's chagrin.
Cut to Malcolm, Reese, and Dewey with friend Stevie in their bedroom remarking that they won't be able to hang out like this anymore. The camera pulls back to show Stevie's Dad who agrees and is more than a little jealous that Malcolm will be making the valedictorian speech at graduation, instead of his son. After he leaves, the boys realize that, now that two of them are moving out, they'll no longer need the "nuclear option." They scramble to the closet, pull out a box with three locks and each open one of the locks. The "option" was a secret they all held which prevented any of them from going too far. The box holds a doctored x-ray. Years ago, the three boys needed to have their poor report cards signed. To distract their Mom, they let her think that she had been diagnosed with cancer. She was so upset that she didn't notice what she was signing. Now, years later, they can destroy the evidence. Dewey is elected to do the deed. Later on, they hold a nighttime ceremony to burn it on the grill. We then see Reese talking to the janitor at school. Reese's so excited that it makes the janitor sad that he'll only have the job for 30 days. Reese is shocked. The job is a union job (with lots of benefits) and after 30 days it becomes impossible to fire someone so new hires are always let go before that happens. Reese reasons that if there were a mess that took longer than 30 days to clean up, he would be safe. So, he starts mixing a barrel of the biggest mess he can create -- made up of dead animals, manure, porta-potty waste, tar, glue, eggs, and so much more.
Francis and wife Piama arrive for graduation day and have given Grandma Ida a ride. Francis is barely talked out of killing the defiant Grandma with a fireplace poker after their long drive. Malcolm receives a letter that his $3,000 piercing grant has been cancelled and it has replaced it with a $50 "students who can't afford college" study. He's now $8,000 short.
Hal is still trying to get the extra money. He tries loan officers at the bank. He even tries a loan shark. Since there's no way he could pay him back, he offers to let the thug go right to the torture and bone-breaking. It could be a good deterrent for future customers. No luck.
Grandma Ida offers to help Reese with his scheme. She advises him to come up with a plan and a scapegoat for the mess. They hide the barrel in the backseat. She'll fake a seizure when they arrive at the graduation ceremony which will give him time to unleash his creation.
The family is preparing for the Kenarbans coming for lunch with their successful friend Cedric Hampton who will be speaking at the graduation later that day. Lois and Francis start arguing about his still not having a job. Lois goes to the closet to get her good china and the old x-ray falls out. Francis grabs it and distracts his Mom so she doesn't see it. He confronts Dewey who says he just couldn't destroy it. It made him too sad. Francis deduces that Dewey loves his brothers and the scam was something that kept them together.
After the meal, Cedric offers Malcolm and Stevie jobs with two-year contracts, six-figure salaries and stock options. Lois emphatically declines for Malcolm and he can't understand it. She tells him that he has to go to college first.
Later, when the whole family's in the car, Malcolm is about to let her have it when Reese's barrel bursts and everyone is covered with the muck. The family is trying to get the stuff off them and are all upset with Reese. Malcom tells his Mom that it's just perfect. He looks exactly like how he feels.
Lois tells him that she wasn't going to let him throw his life away on some big job. That's not the life he's supposed to have. He's going to struggle to get through Harvard, earning every fellowship and internship they have. He's going to graduate first in his and then start working in public service as a district attorney or running some foundation. Then, he'll become governor of some small state and then become president. The family agrees that it's his destiny. They all know it. Their expectations started small but he kept upping the ante. He has no choice. What matters is that he will be the only person in that position that truly gives a crap about people like them. He could go the easy route but then he wouldn't have suffered enough and be a good president. Malcolm's incredulous until his mother tells him to look her in the eye and tell her that he can't do it.
We cut to the graduation and Reese and Malcolm are sitting alone as are their family members in the audience. Though they're all cleaned up, apparently the smell remains. Francis reaches into his suit pocket and an employee badge drops out. Hal sees it and Francis admits that he's had a great job for months now but refuses to tell his Mom and make her happy. He could never live it down.
As Malcolm is being introduced, microphone feedback obscures his last name. Malcolm makes his speech and talks about how they've all been dreaming of this day for a long time, when they gain their independence. But, he tells them, there's no escape. Their families will always be with them in their habits, gestures, etc. They'll never be free but they'll never be alone either. He goes on to quote Paul MacCartney (as his Mother had asked him to) as the scene fades to black.
Flash forward to three months later. Brothers Dewey and Jamie feel close as they hide from a furious Lois. Reese has given roommate Craig a birthday present and baked him a cake. Francis is arguing on the phone with his Mom about finding a job just before kissing his wife and happily heading off to work. Hal is waiting in bed for Lois, so happy that all has worked out -- until Lois enters with a pregnancy test that's tested positive.
Finally, we see Reese in full janitor gear talking to Malcom at Harvard. Reese says that janitor Al was caught with peep holes in the bathroom, so they fired him and brought Reese on fulltime. "Grandma was right, it pays to have a patsy!"
Malcolm's in janitor gear as well. He tells Reese that Harvard is like another world, says goodbye, puts his mop away and heads off to class.