Sam and Gentry are having a talk over Sam saw a Hallucination or not. Gentry is saying that he saw Sam on tape that he was talking to nothing but air. This means that Sam must be sent home and have a bad record. The setting affects the conflict by Sam might be sent home.
Sam talks Gentry to have a hearing with the commander. The commander is very ill and is depressed. Sam has a plan that he can heal the commander, because without the commander the project will fail.
Sam, Gentry, and other professors go and see the commander because Sam says that he can heal the commander back to full health and stop his depression. The general is now being healed by the insects.
Sam and the insects heal the commander and Sam's job is saved. He won't go back home, but promoted so his job will be most important job in the dome.
The commander and Sam are talking about what the insects want and how they could benefit from the insets. Sam comes up with ideas that they build shelters in space so they don't destroy the insects habitat.
In the end we can infer that instead that the people in the dome followed Sam's request and built more settlements in space instead on the planet, destroying the habitat. In conflict is now resolved and the setting of the planet is being affected anymore.