Many of the battles fought west of the Mississippi had Indian participants. Pea Ridge had significant numbers, as did the final "raid" conducted into Missouri in 1864. Foote doesn't go into the politics behind why certain groups of Indians allied themselves with one side or the other, but he does mention that the last group to put down their weapons were Indians in Kirby Smith's Transmississippi, and that they were Trail of Tears veterans as well. He also mentions in passing the hostility of the Five Tribes following the war.

However, the book isn't focused on that. It's focused on the war itself. As a result, a lot of things get mentioned, but it would be on the lines of a couple of paragraphs rather than an entire chapter. Plus, because it is a narrative history, there isn't a high level of analysis of long-ranging consequences.