This song draws its name from how Chris Carrabba got back together with an old friend he had fallen out with though sharing the Ender
books. They read the four books in the series at the same time, and discussing them rekindled the friendship.
Carrabba wrote the song when they weren't getting along, which is what inspired the lyric. After they reconnected, he decided to name the song after the books because they essentially saved their friendship. "Ender" never appears in the lyric.