Charlie returns to the lab with Algernon. He has gone over Nemur’s head and received authorization by the Welberg Foundation to head the investigation into Algernon’s reversion. Nemur is furious but has no other option but to aid Charlie in any way he can. If Charlie cannot come up with an explanation, then Nemur’s entire life’s work will have been proved valueless. If Charlie does determine the cause and can correct it, not only Charlie but Nemur and the rest of the crew will benefit.

After examining Algernon, Burt determines that the mouse has lost much of his ability to problem solve. Charlie wonders if the regression is the result of Algernon being away from the lab for so long. Burt works with Algernon to see exactly at what level the mouse is functioning now. Looking around the lab, Charlie notices one door. Asking Burt what it is, he is told that it is the place where “test subjects” (animals) are frozen and then incinerated. Charlie makes Burt promise that if Algernon should die, the mouse will be given to Charlie rather than be put in the incinerator.

The incinerator makes Charlie wonder what the contingencies are if his own intellectual enhancement proves to be temporary. Nemur reluctantly tells him that if the surgery proves unsuccessful, Charlie will be sent to the Warren state home, with all financial obligations and future living expenses paid for by the Welberg Foundation. Norma, Charlie's sister, insisted on that condition before she granted permission for the surgery. Charlie is furious that he will be sent back to the place from which Mr. Donner had rescued him. Eventually, he sees that it is the most acceptable solution (better than the incinerator, he thinks). He announces to Nemur that he wants to visit the Warren home to see what it is like while he is still able to make some kind of judgment about his future life.

Charlie continues his work at the lab. He refuses Fay permission to visit his workplace, fearing the consequences should Fay and Alice meet each other. He dives deeper into the study of psychology but finds that much of the research is based on “wishful thinking.” This does not give him hope of finding a way to reverse Algernon’s (and perhaps his own) intellectual regression.