LitCharts assigns a color and icon to each theme in Simon vs. the Homo Sapiens Agenda, which you can use to track the themes throughout the work.
Agency and Control
Identity and Assumptions
Relationships and Empathy
Family, Change, and Growing Up
Summary
Analysis
Blue writes to Simon that Blue’s mom took the news relatively well. She's an epidemiologist, so she was mostly concerned with talking about safe sex practices. Blue thanks Simon for giving him the courage to come out. Simon replies that he's proud of Blue, and notes that Blue's parents seem strangely invested in his sex life. He suggests that Blue should only think about sex with someone who likes sentence fragments and accidentally discloses too much personal info.
When Blue thanks Simon, it shows that Blue is also taking confidence from Simon's support. This shows that both boys are learning how to effectively support another person emotionally, while also learning how to be emotionally intimate and vulnerable with someone else. Turning the conversation to sex again makes it clear that Simon and Blue are headed for a sexual coming of age.
Active
Themes
Simon tells Blue about his own coming out experience. He says that now he feels as though he's crossed a border and can't go back. It's exciting and probably good, but he's not sure. When Blue writes back, he says he feels the same way. He suggests that coming out is a one-way process in that you can't go back into the closet after coming out. In closing, Blue assures Simon that he only thinks about sex with people who hide from their girlfriends, eat Oreos, and listen to depressing music.
What Blue and Simon are really getting at with their discussion of coming out is the idea that as one's identity shifts to accommodate new interests or beliefs, that identity will never be the same as it once was. For Simon, this means that even as he's unsettled by how different holidays feel, for example, he'll never be able to go back to how he experienced them as a child.