Hal is about to break a shaving record before being called for breakfast, he remembers its bacon day and rushes to the kitchen tearing his shirt and pants in the process. When he arrives the bacon has all been taken by the boys, he attempts to trick Dewey but Dewey has grown weary of his fathers tricks. Malcolm is feeling strange and could give his father some of his, but it wouldn't stay to the tradition. He then tells his mother he is feeling unusual, but due to Reese copying him Lois doesn't take him seriously and tells him everyone is going to school and work. On Saturday, Malcolm still has side pains and Lois announces they are all going to the hospital after realizing he wasn't faking it.
At the hospital, Hal is petrified due to his phobia of hospitals. Dr. Harrison runs Malcolm's tests and diagnoses him with appendicitis. Malcolm is scheduled for surgery the following day, Malcolm is apprehensive but Lois reassures him he'll be fine, Reese objects saying he saw on TV a man who woke up in the middle of his operation, but he was paralyzed and unable to scream, only terrifying his father more. Lois tells Malcolm staying in the hospital overnight will be far nicer than being at home. However, Malcolm soon learns his stay in the hospital will be anything but pleasant as he is six months too young to have an adult room and must stay in the children's ward. Due to Hal having a phobia of hospitals, Lois decides to take them home and promises she and Hal will be back for Malcolm's operation. Before leaving she forces Reese to hug his brother, Reese complies but whispers to Malcolm if he tells anyone about them hugging Reese will put him right back in the hospital. Once his family leaves, Malcolm is pestered by a young boy, and afterwards Dr. Harrison arrives with a group of medical students to insert Malcolm's IV, forcing a large menacing European orderly named Helmut to hold him down, much to his fear. Malcolm's night is exceptionally worse with scary looking toys, Helmut dragging a body-bag out of the ER, and to top it of, some doctors come in putting a cage on his head to operate on his brain, before realizing their mistake they leave shushing him, Malcolm is left mortified.
At Marlin Academy, Francis persuades his fellow cadets to go on a hunger strike after Commandant Spangler takes away their television. After a day and a half, the cadets show signs of malnourishment. Francis assures them that the hardest part is over and their stomachs have shrunk. After 2 whole days, Commandant Spangler decides to make the cadets earn their rights by torturing them with an omelet bar.
The rest of the family notices the house feels empty without Malcolm, Dewey suggests a board game called March and Conquer (a fictional version of Risk), which they have never been able to enjoy due to Malcolm winning too easily. They all play a nice long game which Lois ends up winning, until Hal demands a rematch, despite it being after midnight already.
At the hospital the next day, Malcolm tells his mother of his endeavors the previous night, Lois assures him it was only a bad dream. Malcolm then learns the family went out to Pancake Pete's for breakfast from playing March and Conquer too late and Lois not having enough energy to cook. Malcolm contemplates being excluded, but Lois says he didn't miss anything and the others were pushover, which they digress towards. They then leave again promising to return in time for the procedure, Malcolm then notices Dewey wearing his shirt, now feeling like the others are doing better without him. Later Dabney, Lloyd and Stevie come to visit Malcolm which he is happy about, although he admits to feeling better now and he may not need his appendix out at all, Lloyd assures him he's sitting on a goldmine and they all talk of rewards they received from their previous procedures.
Hal persuades Lois into another game to prove he and the boys aren't pushovers. Hal, Reese and Dewey gang up on Lois and try outlandish techniques for a pizza delivery as none of them wish to get up to prevent foul play.
Dr. Harrison returns and Malcolm tells him that his blood test may have been incorrect. Dr. Harrison tells the medical students he is a hysterical patient, and shrugs off Malcolm's request for another blood test before leaving, Malcolm is appalled at their behavior and calls after them wondering what's wrong with them and that labs make mistakes, but no one listens to him. Later, Helmut gives Malcolm sedatives as his surgery has been moved up and assures Malcolm his parents were notified. He refuses to take the pills until Helmut forces them down his throat, and knowing he is scared he tells his patient that he needs to let the adults handle things now, Malcolm then spits up his sedatives into his face and runs from the ward to order another blood test, with an enraged Helmut in pursuit of him.
The cadets are famished and think they have proven their point, until they show signs of hallucinations, with Finley not remembering Horton is his roommate and asks him if he'd like to join him on going parasailing after the luau. Eric tells them they're crazy and wonders how they could have a luau while their trapped inside a disabled submarine. Francis tries to motivate them again until Spangler returns and agrees to discuss with Francis. Francis starts hallucinating and goes into the hallway telling the cadets they won the commandants magic hat, Eric asks about the TV, but Francis completely forgot. As a result he is punished by holding golf tees in his mouth while the other cadets enjoy some outside activities and that they don't need the TV, Eric then reminds Francis to replace his divots.
Back at the house, Reese is at an impasse either attacking Lois or Hal, with both telling him that if he attacks either one of them he's grounded, Dewey has hunger pains, and the entire family has forgotten about Malcolm entirely. Reese decides this is the last straw and says he no longer wants to play and the game has never been so terrible, even when Malcolm creamed them. Hal complies and realizes without Malcolm their worst competitive instincts took over. Lois asks if he's quitting, Dewey tells Lois to let it go, calling her by her first name, Lois tells Reese to flip over the board and Hal decides to burn the evil game once and for all.
Malcolm finally makes it to the blood lab, where he convinces a fellow patient to run a blood test for him in exchange for Malcolm's urine to pass off as his own for a drug test. Malcolm reads the blood test results and discovers the truth, then Helmut arrives and carries him off to the operating room, yet while doing so Malcolm tells him what the blood test results were, and if the blood count returns to normal then it isn't appendicitis, most likely, a transient infection or possibly even a cold sore, but Helmut gives him a needle to immobilize him, he requests to talk to Dr. Harrison before being put under. But before the doctors make an incision, they discover Malcolm had written the blood test results on his torso where his appendix is, the doctors now see that their patient was telling the truth all along.
At home, Malcolm is happy, acknowledging that there is nothing like 2 days at the hospital to make him appreciate his own home. Then Lois reveals Malcolm's hospital bill and hate to think how much more i would've been if he'd had the operation. Hal states they can no longer afford a summer vacation and Dewey finds it unfair they all have to pay for Malcolm faking appendicitis. Malcolm tells him he wasn't faking and how he'd proved them wrong, Reese then argues if he's so smart why he didn't figure it out sooner, Hal then wonders if he'd like to answer that for all of them. Malcolm now realizes there's nothing like 10 seconds at home to make him appreciate the hospital.