The episode begins in an abortion clinic. A woman is giving her permission for scientists to use her dead fetus for stem cell research. However, an accident destroys the truck which was carrying all the fetuses from the clinic to Alder Research Group. Cartman happens to be passing by at this moment, and he notices the cargo of the truck. He then steals the fetuses, hoping that he'll be able to resell the fetuses and get a huge profit off of them. He gets distraught, though, when the government makes stem cell research illegal immediately after that.
Meanwhile, the boys find out that Kenny has been diagnosed with a terminal disease, which while not named in the show is confirmed to be muscular dystrophy. Everyone is shocked by the news, (surprisingly, since he dies in nearly every episode before that) and everyone except Stan tries their best to be confident for Kenny's sake. Stan, however, is too upset to be near Kenny in his state, and refuses to even visit him.
Cartman wants to restore stem cell research, and a researcher explains to Cartman about how the studies actually work. With this information, Cartman realizes that the SCR might also be used to help Kenny recover from his illness.
He then thinks that the research could also be used to duplicate a "Shakey's Pizza". The researcher recommends using lumber for that second idea.
Then Cartman gives a very thoughtful speech to the House of Representatives, requesting that the SCR ban be lifted, explaining about his best friend, Kenny, who's slowly dying as they speak. He then says that he believes the research can save Kenny's life. The House of Representatives committee then lifts the ban after Cartman sings "Heat of the Moment". Cartman begins visiting abortion clinics throughout the area, in order to collect even more aborted fetuses.
Meanwhile, after Chef gives Stan a little lecture on death, and why God lets it happen at any given time, Stan finally comes to terms with Kenny dying. He also finds out that Stem Cell Research has been made legal again, and with the hope that a cure might be found, rushes to visit Kenny. Unfortunately, Kenny's hospital room is empty, and the teddy bear he was given is on the floor, seemingly holding onto the unmade bed Kenny slept in. Stan knows what this means - Kyle says he just stopped breathing, and it was over. He also adds that Kenny's last words were "Where's Stan?"
At the funeral, Stan's melancholia has set back in. He even considers himself Kenny's worst friend. As the funeral takes place, though, Cartman comes rushing in and drags Stan and Kyle out of the ceremony, explaining that they have to see the "miracle" that's just occurred. The boys are shocked and disgusted to see that, instead of using the stem cells to save Kenny, Cartman manipulated them into duplicating a Shakey's Pizza. As Kyle beats Cartman up for being so cold-hearted, Stan says "I wasn't Kenny's worst f-f-friend! Cartman was!"