As the third novel in a series, Champion can be seen as the resolution of a three-part epic narrative, a comedy, since it ends with the reunion of Day and June and the promise of a new romance. But that doesn't mean that the novel is without its tragic elements. The center of the novel is that through loyalty to one's friends and loved ones, and a willingness to lay down one's life for the greater good, perhaps peace is possible in America.
The post-apocalyptic aesthetic of the novel is a thin veil covering the obvious allegorical component of the story: It's about political schism in the United States. By pushing the novel into the unknown future, Lu enables herself to talk openly about the divided country. The response to the disease, the invasions, all of it, is simply that heroes must have the resolve to be fearless and sacrifice themselves. Day sacrifices his mind and his body in the quest, willing himself as a servant, even to near-death at the hands of Colonial forces. In this way, he demonstrates love, willingness to die for the good of others.
June also realizes that she can sacrifice for the ones she loves. She does this by giving her blood (a Messianic image) for the healing of nations, including the healing of Day and the hope of a new tomorrow.
By ending with the promise of a new union between the couple, the implication is that their marital bliss is the consequence of each of them following their fate. If either had failed, the nations would not have healed, and their union would be impossible.