Charlotte apparently originally came from some humanian time period before the 21st century but not very far back; her family had their own crypt, which was still standing in the present. (Episode 4.5) The fact that her immune system contained antibodies attuned against smallpox would suggest that Charlotte's home time was sometime before the 1970s. (Episode 4.3)
Charlotte was part of the Time Tribe of Anomaly-travelling nomads who'd met and banded together after becoming lost through the Anomalies, journeying with Emily Merchant and Ethan Dobrowski (real name Patrick Quinn) for three years. Charlotte and Ethan formed a deep and caring relationship, and Charlotte was able to keep Ethan's murderous tendencies under control. (Episode 4.3)
While the Time Tribe were staying in the Cretaceous home of the Tree Creepers, Charlotte fell fatally ill. In hopes of finding medicine to help her, Emily and Ethan separated from the rest of the Tribe and went with Charlotte through an Anomaly to 21st century London. Charlotte died only minutes after they arrived, her last request being that Emily take care of Ethan. The Anomaly Research Centre team discovered her body and apparently had her autopsied and deduced that she, Ethan and Emily were not from the present.
Sometime later, Patrick obtained the ashes of Charlotte's cremated body and placed her urn in her family's crypt.