Let's get one thing out of the way: this ain't light reading, Shmoopers. Sure it's fun to see Charlie achieving his goals, but Daniel Keyes tries to convey a generally somber tone. Check this passage out:
Algernon lies in his own dirt, unmoving, and the odors are stronger than ever before. And what about me? (238)
Keyes sets up the helplessness of Algernon to show the darkness of Charlie's situation. Just this one sentence foreshadows some nasty things to come for Charlie and little Algie—there's not a lot of hope in stinky, dirty cages, but that's exactly the situation Charlie comes up against in the end. After all, he's trapped in his own mind.
It gets even darker when Charlie's intelligence starts to plummet:
Downhill. Thoughts of suicide to stop it all now while I am still in control and aware of the world around me. (17.278)
Charlie doesn't have a whole lot of options for escape, and he makes it pretty clear just how upsetting that is to him. While he doesn't commit suicide, it's only a matter of time before his life and mind spiral out of control. This is tough reading, Shmoopers, but it helps us understand the scary places Charlie has to go to conquer his demons. If we read with the knowledge of how hopeless his situation really is the few bright moments he has with Alice seem all the more influential in his life. There's no happy ending to be had, but silver linings are all over the place.