I read it in the past few years. I think the “aliens” were called indigenes. Main characters are a man and a woman who end up unraveling a conspiracy through their travels to the new planet where they find the aliens living underground. They used to live above ground until the humans showed up and terraformed their planet making the atmosphere unbreathable for them. One was curious about humans and he would use a disguise (they resembled humans but had translucent skin) and a breathing device in his throat to allow him ventures into the human settlement. He caught the attention of a child that he continued to meet with so he could learn about humans. The main female character gets hurt somehow and the “aliens” help her with a treatment that ends up almost killing her. As it turns out, it was not dna compatible so it was transforming her to one of the aliens. And long story short, we learn that the “aliens” are modified humans put on the planet a hundred (?) years earlier as a last ditch effort to save humankind. But in the years since they were put on the planet, humans developed the tech and understanding needed to transform the planet so they could colonize it. Very few knew about the “indigenes” and the attempted genocide.