Charlie and Algernon return to Beekman. Charlie has received approval from the Welberg Foundation to conduct an independent study of his project. The laboratory staff has been ordered to assist him with his project, but they are skeptical of his abilities.
Algernon is displaying a loss of problem-solving skills. He is reverting back to a more primitive level. Charlie offers other explanations for Algernon's inability to run the maze, but inherently he knows that time is an enemy.
While acquainting himself with the equipment and the re-sources of the lab, Charlie notices that one room is marked as off limits. Burt explains that this room contains the freezer and the incinerator. To reduce odors, laboratory animals are frozen before the staff disposes of them. Charlie requests that this room not be Algernon's fate; Charlie will take care of Algernon when the mouse dies. Reflecting on his own situation, Charlie wonders what will be-come of him. Burt informs him that preparations have already been made for Charlie to enter the Warren State Home and Training School. Charlie requests that a visit to the home be arranged, because he wants to see what his future holds while he can still understand it.
Charlie returns to the lab on his own terms. He has contacted the Welberg Foundation, which agrees to allow him to participate in the analysis of his study. By setting up this arrangement, Charlie keeps control of his life and forces those around him to regard him as more than a lab specimen.
Working as a peer, Charlie learns the details of his experiment. He discovers that most lab specimens are incinerated; however, he requests that Algernon be given to him for a proper burial when Algernon dies. Charlie is also surprised to learn arrangements have been made for him to move to the Warren State Home if the experiment concludes with Charlie's regression. This twist of fate is ironic: Charlie was thrown out of his own home and thought to be placed in the Warren State Home because of his sister. Now, with the permission his sister gave for his participation in this experiment, she is again essentially responsible for his sentencing to Warren.
Keyes uses the maze imagery to bring Charlie's odyssey as a "lab animal" full circle. Charlie wants to visit the Warren Home so that he can know his future: "I see now that the path I take through the maze makes me what I am. . . . [K]nowing the paths I have followed and the ones left to take will help me understand what I am becoming." Charlie accepts his experimental role and ennobles it by his willing participation.