Ishmael is a gorilla who was captured in the wild as a youth and has spent his adult life in various forms of captivity. During captivity, he grows more and more self-aware and eventually comes under the care of Walter Sokolow, who encourages his intellectual growth through their telepathic communication. Ishmael becomes a teacher whose focus is on how to save the world and challenges his students with his intellect, obstinacy, and pride, and his hope for the human race, despite the challenges facing it.
Throughout the novel, Ishmael is used as a distancing mechanism by the author; Quinn puts his own philosophical theories in the mouth of a gorilla to upset readers' expectations about and biases against other life-forms and their intelligence. Ishmael, having spent his life in captivity, has learned to question captivity; thus, he tries to teach his captors (humans) what he's learned about them through his studies. Through his research on human history, he's come to see that they, too, are captive to a destructive way of life in their pursuit of domination over the rest of the world.
Through his studies, Ishmael tries to understand why humans feel called to dominate the world, and he teaches the explanation he's come up with to his student (the narrator). Ishmael speaks as a symbol of the sentience and intelligence of the rest of the world's life-forms that humans (at least humans in the "Taker" cultures — that is, basically everyone except for tribal cultures) have dismissed, because they see themselves as superior and removed from the rules that structure the evolution and survival of other life-forms on the planet.