Bullying
The story begins with an allegory about two friends who are surrounded by a group of bullies. The bullies are a group, so they are more powerful, and they bully Austin and Robby although the two boys were minding their business. The bullies can be seen as a metaphor for powerful people who exploit less powerful people by teaming up on them. Perhaps this also has thematic connections to the government because of later parts of the novel where soldiers and the military are mentioned.
Friendship
Austin and Robby are friends who become closer through their shared suffering. They are bullied together, so they can sympathize with each other. Just like the bullies find power in numbers, so also Austin and Robby find power in their friendship, because they don't have to be alone. They are partners in crime, so to speak, and thematically their friendship speaks of the importance of friendship and honesty.
Descending into chaos
When the boys return from the roof through a passage into the boss's office, that can be seen as a symbolic descent into chaos. Sure enough, when they find the vial with the virus in it, the whole community descends into chaos, because the plague is released into the neighborhood. The chaos saves them from being beaten up by the bully, but it brings a new problem that makes the whole community have to work together.
The plague
The plague is a stand in threat that the boys are unable to process alone. They can't be private about the plague because the threat is too great. It makes their story public, whereas before their suffering was private. They are forced to collaborate with their community, so that the plague can be seen as an important symbol for shared suffering and the universal problems that humans have to face together.
The shelter called Eden
The fact that the book ends with Eden is an inversion of the book the reference alludes to; in the Bible, the story of Eden comes first. The reversal is symbolic, suggesting that heaven is actually when a community comes together to support and help one another. Ironically, it doesn't mean that they aren't suffering or that threats have been eliminated. Instead, it means they are suffering together and taking each challenge as a team, and that restores something Edenic.
