Yeah, I can't say this is entirely surprising, and the bittersweet aspects of it fits the rest of the story, yet even so it's melancholy. Yet at the same time, he's gotten to enjoy a beautiful world in ways they probably didn't imagine, and see a lot of interesting things. Maybe the story will do a turn around, but it could also take the "ends are also part of life route", would being truly immortal even be that enjoyable? And if humans did return a use him for war that'd suck too, he'd end successful in his mission and free of it all.
Guess we'll see, and it's fun to have a bit more history of the world revealed. Maybe there is still a significant amount of remaining pollution in some areas, though the modern forms of inhabitants can't really recognize it as things continue to slowly recover. Shades of series like Nausicaä or Ergo Proxy.