Charlie likes Algernon from the start but at first feels bad when the mouse beats him at the maze games they are both asked to play. He wonders why the mouse is so smart and speculates it might be because he is a white mouse. He begins to feel a bond with the mouse when he finds out that they both have motivation.
After the operation, Charlie continues to bond and identify with Algernon because they both have been subjected to the same surgery to improve their intellects. The identification becomes bitter as Charlie grows to understand they were both used to advance Dr. Nemur's agenda. Dr. Nemur, aging, and wanting a last success, jumped too rapidly into the brain operation, which Charlie realizes will leave both he and Algernon worse off than before as their intellects will rapidly decline. He recognizes he has been used as no more than an experimental lab animal. He mourns when Algernon dies because he identifies so strongly with him.