@tonygodsdusk Looks like the teacher was legitimately in love with her, so he used his final chance to screw her on graduation day. At the end he's crying and saying that now he can "graduate" from her, so it's a graduation ceremony for both of them. The last page has the girl thinking "Sensei, thank you for those three years" (lit. "I was in your care for three years").
Kinda typical hentai plot, but we have probably all seen or heard about people doing dumb things because of love, so I'd say it's not that far-fetched. The guy even sounds like an actual good, honest teacher outside of that event.