“So you’re not taken from me again and neither is your mother,” Noah says.
Noah is Charlotte’s father, and Charlotte’s mother is her own daughter Elizabeth. At the end of season two, we see that Young Noah and Young Elizabeth are in the bunker together when the Apocalypse happens. Presumably they grow older together and eventually Elizabeth got pregnant with Charlotte. Sometime after Charlotte was born, she was taken by an unknown person and brought back in time.
Charlotte was raised by H.G. Tannhaus, never knowing who (or where or when) her parents were. She then got together with Peter, and they had Franziska and Elisabeth — who’s both Charlotte’s daughter and mother.
“I promised her I’d bring you back,” Noah says. “I’ve looked for you all these years. But you were here the entire time. Adam knew it was you, he knew it the whole time. He is preparing for what comes afterwards. I read the last pages. The nuclear plant, Jonas — it’ll all happen again. The apocalypse … in two days. But I now know what I must do. I have to end Adam, so everyone lives. Not just those in the bunker.”
Noah realizing Adam had the answer to his search the entire time was the breaking point. But Noah failed to kill Adam, and was instead shot and killed by his sister Agnes.